Merge branch 'dev'
This commit is contained in:
Heng Li
commit
b8e189c1e5
38
NEWS.md
38
NEWS.md
|
|
@ -1,34 +1,37 @@
|
|||
Release 0.7.11 (XX November, 2014)
|
||||
-----------------------------------
|
||||
Release 0.7.11 (23 December, 2014)
|
||||
----------------------------------
|
||||
|
||||
A major change to BWA-MEM is the support of mapping to ALT contigs in addition
|
||||
to the primary assembly. Part of the ALT mapping strategy is implemented in
|
||||
BWA-MEM and the rest in a postprocessing script for now. Due to the extra
|
||||
layer of complexity on generating the reference genome and on the two-step
|
||||
mapping, we start to provide a wrapper script and precompiled binaries since
|
||||
this release. Please check README-alt.md for details.
|
||||
this release. The package may be more convenient to some specific use cases.
|
||||
For general uses, the single BWA binary still works like the old way.
|
||||
|
||||
Another major addition to BWA-MEM is HLA typing, which made possible with the
|
||||
new ALT mapping strategy. Necessary data and programs are included in the
|
||||
binary release. The wrapper script also performs HLA typing when HLA genes are
|
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also included in the reference genome as additional ALT contigs.
|
||||
binary release. The wrapper script also optionally performs HLA typing when HLA
|
||||
genes are included in the reference genome as additional ALT contigs.
|
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|
||||
Other notable changes to BWA-MEM:
|
||||
|
||||
* Added option `-b` to `bwa index`. This option tunes the batch size used in
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||||
the construction of BWT. It is advised to use large `-b` for huge reference
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||||
sequences such as the *nt* database.
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||||
sequences such as the BLAST *nt* database.
|
||||
|
||||
* Optimized for PacBio data. This includes a change to the scoring based on a
|
||||
mini-study done by Aaron Quinlan and a heuristic speedup. Further speedup is
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||||
* Optimized for PacBio data. This includes a change to scoring based on a
|
||||
study done by Aaron Quinlan and a heuristic speedup. Further speedup is
|
||||
possible, but needs more careful investigation.
|
||||
|
||||
* Dropped PacBio read-to-read alignment for now. BWA-MEM is only good at
|
||||
finding the best hit, not all hits. Option `-x pbread` is still available,
|
||||
but hidden on the command line.
|
||||
* Dropped PacBio read-to-read alignment for now. BWA-MEM is good for finding
|
||||
the best hit, but is not very sensitive to suboptimal hits. Option `-x pbread`
|
||||
is still available, but hidden on the command line. This may be removed in
|
||||
future releases.
|
||||
|
||||
* Added a new pre-setting for Oxford Nanopore 2D reads. LAST is still a little
|
||||
more sensitive on bacterial data, but bwa-mem is times faster on human data.
|
||||
more sensitive on older bacterial data, but bwa-mem is as good on more
|
||||
recent data and is times faster for mapping against mammalian genomes.
|
||||
|
||||
* Added LAST-like seeding. This improves the accuracy for longer reads.
|
||||
|
||||
|
|
@ -44,7 +47,16 @@ Other notable changes to BWA-MEM:
|
|||
writing SAM. This saves significant wall-clock time when reading from
|
||||
or writing to a slow Unix pipe.
|
||||
|
||||
(0.7.11: XX November 2014, rXXX)
|
||||
With the new release, the recommended way to map Illumina reads to GRCh38 is to
|
||||
use the bwakit binary package:
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||||
|
||||
bwa.kit/run-gen-ref hs38DH
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bwa.kit/bwa index hs38DH.fa
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||||
bwa.kit/run-bwamem -t8 -H -o out-prefix hs38DH.fa read1.fq.gz read2.fq.gz | sh
|
||||
|
||||
Please check bwa.kit/README.md for details and command line options.
|
||||
|
||||
(0.7.11: 23 December 2014, r1034)
|
||||
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -5,10 +5,10 @@
|
|||
wget -O- http://sourceforge.net/projects/bio-bwa/files/bwakit/bwakit-0.7.11_x64-linux.tar.bz2/download \
|
||||
| gzip -dc | tar xf -
|
||||
# Generate the GRCh38+ALT+decoy+HLA and create the BWA index
|
||||
bwa.kit/run-gen-ref hs38d6 # download GRCh38 and write hs38d6.fa
|
||||
bwa.kit/bwa index hs38d6.fa # create BWA index
|
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bwa.kit/run-gen-ref hs38DH # download GRCh38 and write hs38DH.fa
|
||||
bwa.kit/bwa index hs38DH.fa # create BWA index
|
||||
# mapping
|
||||
bwa.kit/run-bwamem -o out hs38d6.fa read1.fq read2.fq | sh # skip "|sh" to show command lines
|
||||
bwa.kit/run-bwamem -o out -H hs38DH.fa read1.fq read2.fq | sh # skip "|sh" to show command lines
|
||||
```
|
||||
|
||||
This generates `out.aln.bam` as the final alignment, `out.hla.top` for best HLA
|
||||
|
|
@ -94,11 +94,11 @@ CHM1 short reads and present also in NA12878. You can try [BLAT][blat] or
|
|||
|
||||
For a more complete reference genome, we compiled a new set of decoy sequences
|
||||
from GenBank clones and the de novo assembly of 254 public [SGDP][sgdp] samples.
|
||||
The sequences are included in `hs38d6-extra.fa` from the [BWA binary
|
||||
The sequences are included in `hs38DH-extra.fa` from the [BWA binary
|
||||
package][res].
|
||||
|
||||
In addition to decoy, we also put multiple alleles of HLA genes in
|
||||
`hs38d6-extra.fa`. These genomic sequences were acquired from [IMGT/HLA][hladb],
|
||||
`hs38DH-extra.fa`. These genomic sequences were acquired from [IMGT/HLA][hladb],
|
||||
version 3.18.0 and are used to collect reads sequenced from these genes.
|
||||
|
||||
### HLA typing
|
||||
|
|
@ -125,26 +125,26 @@ most of them are distributed under restrictive licenses.
|
|||
|
||||
To check whether GRCh38 is better than GRCh37, we mapped the CHM1 and NA12878
|
||||
unitigs to GRCh37 primary (hs37), GRCh38 primary (hs38) and GRCh38+ALT+decoy
|
||||
(hs38d6), and called small variants from the alignment. CHM1 is haploid.
|
||||
(hs38DH), and called small variants from the alignment. CHM1 is haploid.
|
||||
Ideally, heterozygous calls are false positives (FP). NA12878 is diploid. The
|
||||
true positive (TP) heterozygous calls from NA12878 are approximately equal
|
||||
to the difference between NA12878 and CHM1 heterozygous calls. A better assembly
|
||||
should yield higher TP and lower FP. The following table shows the numbers for
|
||||
these assemblies:
|
||||
|
||||
|Assembly|hs37 |hs38 |hs38d6|CHM1_1.1| huref|
|
||||
|Assembly|hs37 |hs38 |hs38DH|CHM1_1.1| huref|
|
||||
|:------:|------:|------:|------:|------:|------:|
|
||||
|FP | 255706| 168068| 142516|307172 | 575634|
|
||||
|TP |2142260|2163113|2150844|2167235|2137053|
|
||||
|
||||
With this measurement, hs38 is clearly better than hs37. Genome hs38d6 reduces
|
||||
With this measurement, hs38 is clearly better than hs37. Genome hs38DH reduces
|
||||
FP by ~25k but also reduces TP by ~12k. We manually inspected variants called
|
||||
from hs38 only and found the majority of them are associated with excessive read
|
||||
depth, clustered variants or weak alignment. We believe most hs38-only calls are
|
||||
problematic. In addition, if we compare two NA12878 replicates from HiSeq X10
|
||||
with nearly identical library construction, the difference is ~140k, an order
|
||||
of magnitude higher than the difference between hs38 and hs38d6. ALT contigs,
|
||||
decoy and HLA genes in hs38d6 improve variant calling and enable the analyses of
|
||||
of magnitude higher than the difference between hs38 and hs38DH. ALT contigs,
|
||||
decoy and HLA genes in hs38DH improve variant calling and enable the analyses of
|
||||
ALT contigs and HLA typing at little cost.
|
||||
|
||||
## Problems and Future Development
|
||||
|
|
|
|||
53
bwa.1
53
bwa.1
|
|
@ -1,4 +1,4 @@
|
|||
.TH bwa 1 "18 November 2014" "bwa-0.7.11-r999" "Bioinformatics tools"
|
||||
.TH bwa 1 "23 December 2014" "bwa-0.7.11-r1034" "Bioinformatics tools"
|
||||
.SH NAME
|
||||
.PP
|
||||
bwa - Burrows-Wheeler Alignment Tool
|
||||
|
|
@ -75,7 +75,7 @@ appropriate algorithm will be chosen automatically.
|
|||
.TP
|
||||
.B mem
|
||||
.B bwa mem
|
||||
.RB [ -aCHMpP ]
|
||||
.RB [ -aCHjMpP ]
|
||||
.RB [ -t
|
||||
.IR nThreads ]
|
||||
.RB [ -k
|
||||
|
|
@ -88,6 +88,12 @@ appropriate algorithm will be chosen automatically.
|
|||
.IR seedSplitRatio ]
|
||||
.RB [ -c
|
||||
.IR maxOcc ]
|
||||
.RB [ -D
|
||||
.IR chainShadow ]
|
||||
.RB [ -m
|
||||
.IR maxMateSW ]
|
||||
.RB [ -W
|
||||
.IR minSeedMatch ]
|
||||
.RB [ -A
|
||||
.IR matchScore ]
|
||||
.RB [ -B
|
||||
|
|
@ -102,6 +108,8 @@ appropriate algorithm will be chosen automatically.
|
|||
.IR unpairPen ]
|
||||
.RB [ -R
|
||||
.IR RGline ]
|
||||
.RB [ -H
|
||||
.IR HDlines ]
|
||||
.RB [ -v
|
||||
.IR verboseLevel ]
|
||||
.I db.prefix
|
||||
|
|
@ -193,9 +201,28 @@ Discard a MEM if it has more than
|
|||
.I INT
|
||||
occurence in the genome. This is an insensitive parameter. [500]
|
||||
.TP
|
||||
.BI -D \ INT
|
||||
Drop chains shorter than
|
||||
.I FLOAT
|
||||
fraction of the longest overlapping chain [0.5]
|
||||
.TP
|
||||
.BI -m \ INT
|
||||
Perform at most
|
||||
.I INT
|
||||
rounds of mate-SW [50]
|
||||
.TP
|
||||
.BI -W \ INT
|
||||
Drop a chain if the number of bases in seeds is smaller than
|
||||
.IR INT .
|
||||
This option is primarily used for longer contigs/reads. When positive, it also
|
||||
affects seed filtering. [0]
|
||||
.TP
|
||||
.B -P
|
||||
In the paired-end mode, perform SW to rescue missing hits only but do not try to find
|
||||
hits that fit a proper pair.
|
||||
|
||||
.TP
|
||||
.B SCORING OPTIONS:
|
||||
.TP
|
||||
.BI -A \ INT
|
||||
Matching score. [1]
|
||||
|
|
@ -244,15 +271,30 @@ and will be converted to a TAB in the output SAM. The read group ID will be
|
|||
attached to every read in the output. An example is '@RG\\tID:foo\\tSM:bar'.
|
||||
[null]
|
||||
.TP
|
||||
.BI -H \ ARG
|
||||
If ARG starts with @, it is interpreted as a string and gets inserted into the
|
||||
output SAM header; otherwise, ARG is interpreted as a file with all lines
|
||||
starting with @ in the file inserted into the SAM header. [null]
|
||||
.TP
|
||||
.BI -T \ INT
|
||||
Don't output alignment with score lower than
|
||||
.IR INT .
|
||||
This option affects output and occasionally SAM flag 2. [30]
|
||||
.TP
|
||||
.BI -h \ INT
|
||||
.BI -j
|
||||
Treat ALT contigs as part of the primary assembly (i.e. ignore the
|
||||
.I db.prefix.alt
|
||||
file).
|
||||
.TP
|
||||
.BI -h \ INT[,INT2]
|
||||
If a query has not more than
|
||||
.I INT
|
||||
hits with score higher than 80% of the best hit, output them all in the XA tag [5]
|
||||
hits with score higher than 80% of the best hit, output them all in the XA tag.
|
||||
If
|
||||
.I INT2
|
||||
is specified, BWA-MEM outputs up to
|
||||
.I INT2
|
||||
hits if the list contains a hit to an ALT contig. [5,200]
|
||||
.TP
|
||||
.B -a
|
||||
Output all found alignments for single-end or unpaired paired-end reads. These
|
||||
|
|
@ -572,6 +614,7 @@ R 0x0020 strand of the mate
|
|||
s 0x0100 the alignment is not primary
|
||||
f 0x0200 QC failure
|
||||
d 0x0400 optical or PCR duplicate
|
||||
S 0x0800 supplementary alignment
|
||||
.TE
|
||||
|
||||
.PP
|
||||
|
|
@ -605,8 +648,6 @@ _
|
|||
XS Suboptimal alignment score
|
||||
XF Support from forward/reverse alignment
|
||||
XE Number of supporting seeds
|
||||
_
|
||||
XP Alt primary hits; format: /(chr,pos,CIGAR,mapQ,NM;)+/
|
||||
.TE
|
||||
|
||||
.PP
|
||||
|
|
|
|||
|
|
@ -17,14 +17,14 @@ other programs or use data in `bwa.kit`. The following shows an example about
|
|||
how to use bwakit:
|
||||
|
||||
```sh
|
||||
# Download bwakit (or from <http://sourceforge.net/projects/bio-bwa/files/bwakit/> manually)
|
||||
# Download the bwa-0.7.11 binary package (download link may change)
|
||||
wget -O- http://sourceforge.net/projects/bio-bwa/files/bwakit/bwakit-0.7.11_x64-linux.tar.bz2/download \
|
||||
| gzip -dc | tar xf -
|
||||
# Generate the GRCh38+ALT+decoy+HLA and create the BWA index
|
||||
bwa.kit/run-gen-ref hs38d6 # download GRCh38 and write hs38d6.fa
|
||||
bwa.kit/bwa index hs38d6.fa # create BWA index
|
||||
bwa.kit/run-gen-ref hs38DH # download GRCh38 and write hs38DH.fa
|
||||
bwa.kit/bwa index hs38DH.fa # create BWA index
|
||||
# mapping
|
||||
bwa.kit/run-bwamem -o out hs38d6.fa read1.fq read2.fq | sh
|
||||
bwa.kit/run-bwamem -o out -H hs38DH.fa read1.fq read2.fq | sh
|
||||
```
|
||||
|
||||
The last mapping command line will generate the following files:
|
||||
|
|
@ -44,13 +44,37 @@ Bwakit can be [downloaded here][res]. It is only available to x86_64-linux. The
|
|||
scripts in the package are available in the [bwa/bwakit][kit] directory.
|
||||
Packaging is done manually for now.
|
||||
|
||||
## Contents
|
||||
## Limitations
|
||||
|
||||
* HLA typing only works for high-coverage human data. The typing accuracy can
|
||||
still be improved. We encourage researchers to develop better HLA typing tools
|
||||
based on the intermediate output of bwakit (for each HLA gene included in the
|
||||
index, bwakit writes all reads matching it in a separate file).
|
||||
|
||||
* Duplicate marking only works when all reads from a single paired-end library
|
||||
are provided as the input. This limitation is the necessary tradeoff of fast
|
||||
MarkDuplicate provided by samblaster.
|
||||
|
||||
* The adapter trimmer is chosen as it is fast, pipe friendly and does not
|
||||
discard reads. However, it is conservative and suboptimal. If this is a
|
||||
concern, it is recommended to preprocess input reads with a more sophisticated
|
||||
adapter trimmer. We also hope existing trimmers can be modified to operate on
|
||||
an interleaved FASTQ stream. We will replace trimadap once a better trimmer
|
||||
meets our needs.
|
||||
|
||||
* Bwakit can be memory demanding depends on the functionality invoked. For 30X
|
||||
human data, bwa-mem takes about 11GB RAM with 32 threads, samblaster uses
|
||||
close to 10GB and BAM shuffling (if the input is sorted BAM) uses several GB.
|
||||
In the current setting, sorting uses about 10GB.
|
||||
|
||||
|
||||
## Package Contents
|
||||
```
|
||||
bwa.kit
|
||||
|-- README.md This README file.
|
||||
|-- run-bwamem *Entry script* for the entire mapping pipeline.
|
||||
|-- bwa *BWA binary*
|
||||
|-- k8 Interpreter for *.js scripts.
|
||||
|-- k8 Interpretor for *.js scripts.
|
||||
|-- bwa-postalt.js Post-process alignments to ALT contigs/decoys/HLA genes.
|
||||
|-- htsbox Used by run-bwamem for shuffling BAMs and BAM=>FASTQ.
|
||||
|-- samblaster MarkDuplicates for reads from the same library. v0.1.20
|
||||
|
|
@ -60,10 +84,8 @@ bwa.kit
|
|||
|
|
||||
|-- run-gen-ref *Entry script* for generating human reference genomes.
|
||||
|-- resource-GRCh38 Resources for generating GRCh38
|
||||
| |-- hs38d6-decoy.nt.anno Top decoy-to-nt hits. Not used by any scripts.
|
||||
| |-- hs38d6-decoy.rm.out RepeatMasker report. Not used.
|
||||
| |-- hs38d6-extra.fa Decoy and HLA gene sequences. Used by run-gen-ref.
|
||||
| `-- hs38d6.fa.alt ALT-to-GRCh38 alignment. Used by run-gen-ref.
|
||||
| |-- hs38DH-extra.fa Decoy and HLA gene sequences. Used by run-gen-ref.
|
||||
| `-- hs38DH.fa.alt ALT-to-GRCh38 alignment. Used by run-gen-ref.
|
||||
|
|
||||
|-- run-HLA HLA typing for sequences extracted by bwa-postalt.js.
|
||||
|-- typeHLA.sh Type one HLA-gene. Called by run-HLA.
|
||||
|
|
|
|||
|
|
@ -18,29 +18,38 @@ Options: -o STR prefix for output files [inferred from
|
|||
ont2d: Oxford Nanopore reads (~10kb query, higher error rate)
|
||||
-t INT number of threads [1]
|
||||
|
||||
-H apply HLA typing
|
||||
-a trim HiSeq2000/2500 PE resequencing adapters (via trimadap)
|
||||
-d mark duplicate (via samblaster)
|
||||
-S for SAM/BAM input, don\'t shuffle
|
||||
-s sort the output alignment (requring more RAM)
|
||||
-H skip HLA typing
|
||||
-S for BAM input, don\'t shuffle
|
||||
-s sort the output alignment (via samtools; requring more RAM)
|
||||
-k keep temporary files generated by typeHLA
|
||||
|
||||
Examples:
|
||||
|
||||
* Map paired-end reads to GRCh38+ALT+decoy+HLA and perform HLA typing:
|
||||
|
||||
run-bwamem -o prefix -t8 -R"@RG\tID:foo\tSM:bar" hs38d6.fa read1.fq.gz read2.fq.gz
|
||||
run-bwamem -o prefix -t8 -HR"@RG\tID:foo\tSM:bar" hs38DH.fa read1.fq.gz read2.fq.gz
|
||||
|
||||
Note: HLA typing is only effective for high-coverage data. The typing accuracy varies
|
||||
with the quality of input. It is only intended for research purpose, not for diagnostic.
|
||||
|
||||
* Remap coordinate-sorted BAM, transfer read groups tags, trim Illumina PE adapters and
|
||||
sort the output. The BAM may contain single-end or paired-end reads, or a mixture of
|
||||
the two types. Specifying -R stops read group transfer.
|
||||
|
||||
run-bwamem -sao prefix hs38d6.fa old-srt.bam
|
||||
run-bwamem -sao prefix hs38DH.fa old-srt.bam
|
||||
|
||||
* Remap name-grouped BAM and mark duplicates. Note that in this case, all reads from
|
||||
a single library should be aligned at the same time. Paired-end only.
|
||||
Note: the adaptor trimmer included in bwa.kit is chosen because it fits the current
|
||||
mapping pipeline better. It is conservative and suboptimal. A more sophisticated
|
||||
trimmer is recommended if this becomes a concern.
|
||||
|
||||
run-bwamem -Sdo prefix hs38d6.fa old-unsrt.bam
|
||||
* Remap name-grouped BAM and mark duplicates:
|
||||
|
||||
run-bwamem -Sdo prefix hs38DH.fa old-unsrt.bam
|
||||
|
||||
Note: streamed duplicate marking requires all reads from a single paired-end library
|
||||
to be aligned at the same time.
|
||||
|
||||
Output files:
|
||||
|
||||
|
|
@ -84,7 +93,7 @@ if (defined $opts{o}) {
|
|||
} elsif ($ARGV[1] =~ /^(\S+)\.(fastq|fq|fasta|fa|mag|mag\.gz|fasta\.gz|fa\.gz|fastq\.gz|fq\.gz|bam)$/) {
|
||||
$prefix = $1;
|
||||
}
|
||||
die("ERROR: failed to identify the prefix for output. Please specify -p.\n") unless defined($prefix);
|
||||
die("ERROR: failed to identify the prefix for output. Please specify -o.\n") unless defined($prefix);
|
||||
|
||||
my $size = 0;
|
||||
my $comp_ratio = 3.;
|
||||
|
|
@ -156,9 +165,9 @@ if (-f "$ARGV[0].alt") {
|
|||
my $t_sort = $opts{t} < 4? $opts{t} : 4;
|
||||
$cmd .= defined($opts{s})? " | $root/samtools sort -@ $t_sort -m1G - $prefix.aln;\n" : " | $root/samtools view -1 - > $prefix.aln.bam;\n";
|
||||
|
||||
if ($has_hla && !defined($opts{H}) && (!defined($opts{x}) || $opts{x} eq 'intractg')) {
|
||||
if ($has_hla && defined($opts{H}) && (!defined($opts{x}) || $opts{x} eq 'intractg')) {
|
||||
$cmd .= "$root/run-HLA ". (defined($opts{x}) && $opts{x} eq 'intractg'? "-A " : "") . "$prefix.hla > $prefix.hla.top 2> $prefix.log.hla;\n";
|
||||
$cmd .= "cat $prefix.hla.HLA*.gt | grep ^GT | cut -f2- > $prefix.hla.all;\n";
|
||||
$cmd .= "touch $prefix.hla.HLA-dummy.gt; cat $prefix.hla.HLA*.gt | grep ^GT | cut -f2- > $prefix.hla.all;\n";
|
||||
$cmd .= "rm -f $prefix.hla.HLA*;\n" unless defined($opts{k});
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -6,16 +6,25 @@ url38="ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals
|
|||
url37d5="ftp://ftp.ncbi.nlm.nih.gov/1000genomes/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz"
|
||||
|
||||
if [ $# -eq 0 ]; then
|
||||
echo "Usage: $0 <hs38|hs38a|hs38d6|hs37|hs37d5>"
|
||||
echo "Usage: $0 <hs38|hs38a|hs38DH|hs37|hs37d5>"
|
||||
echo "Analysis sets:"
|
||||
echo " hs38 primary assembly of GRCh38 (incl. chromosomes, unplaced and unlocalized contigs) and EBV"
|
||||
echo " hs38a hs38 plus ALT contigs"
|
||||
echo " hs38DH hs38a plus decoy contigs and HLA genes (recommended for GRCh38 mapping)"
|
||||
echo " hs37 primary assembly of GRCh37 (used by 1000g phase 1) plus the EBV genome"
|
||||
echo " hs37d5 hs37 plus decoy contigs (used by 1000g phase 3)"
|
||||
echo ""
|
||||
echo "Note: This script downloads human reference genomes. For hs38a and hs38DH, it needs additional"
|
||||
echo " sequences and ALT-to-REF mapping included in the bwa.kit package."
|
||||
exit 1;
|
||||
fi
|
||||
|
||||
if [ $1 == "hs38d6" ]; then
|
||||
(wget -O- $url38 | gzip -dc; cat $root/resource-GRCh38/hs38d6-extra.fa) > $1.fa
|
||||
[ ! -f $1.fa.alt ] && cp $root/resource-GRCh38/hs38d6.fa.alt $1.fa.alt
|
||||
if [ $1 == "hs38DH" ]; then
|
||||
(wget -O- $url38 | gzip -dc; cat $root/resource-GRCh38/hs38DH-extra.fa) > $1.fa
|
||||
[ ! -f $1.fa.alt ] && cp $root/resource-GRCh38/hs38DH.fa.alt $1.fa.alt
|
||||
elif [ $1 == "hs38a" ]; then
|
||||
wget -O- $url38 | gzip -dc > $1.fa
|
||||
[ ! -f $1.fa.alt ] && grep _alt $root/resource-GRCh38/hs38d6.fa.alt > $1.fa.alt
|
||||
[ ! -f $1.fa.alt ] && grep _alt $root/resource-GRCh38/hs38DH.fa.alt > $1.fa.alt
|
||||
elif [ $1 == "hs38" ]; then
|
||||
wget -O- $url38 | gzip -dc | awk '/^>/{f=/_alt/?0:1}f' > $1.fa
|
||||
elif [ $1 == "hs37d5" ]; then
|
||||
|
|
|
|||
|
|
@ -15,6 +15,7 @@ fi
|
|||
preres="resource-human-HLA"
|
||||
root=`dirname $0`
|
||||
pre=$1.$2
|
||||
touch $pre.gt
|
||||
|
||||
if [ ! -s $pre.fq ]; then
|
||||
echo '** Empty input file. Abort!' >&2
|
||||
|
|
|
|||
|
|
@ -268,7 +268,7 @@ int main_mem(int argc, char *argv[])
|
|||
fprintf(stderr, " -p smart pairing (ignoring in2.fq)\n");
|
||||
fprintf(stderr, " -R STR read group header line such as '@RG\\tID:foo\\tSM:bar' [null]\n");
|
||||
fprintf(stderr, " -H STR/FILE insert STR to header if it starts with @; or insert lines in FILE [null]\n");
|
||||
fprintf(stderr, " -j ignore ALT contigs\n");
|
||||
fprintf(stderr, " -j treat ALT contigs as part of the primary assembly (i.e. ignore <idxbase>.alt file)\n");
|
||||
fprintf(stderr, "\n");
|
||||
fprintf(stderr, " -v INT verbose level: 1=error, 2=warning, 3=message, 4+=debugging [%d]\n", bwa_verbose);
|
||||
fprintf(stderr, " -T INT minimum score to output [%d]\n", opt->T);
|
||||
|
|
|
|||
Loading…
Reference in New Issue