zzh
/
fast-bwa
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

updated directory name

This commit is contained in:
Heng Li 2014-10-21 00:57:06 -04:00
parent 4260699a09
commit 574098d034
1 changed files with 5 additions and 5 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

10
README-alt.md
View File

@ -14,13 +14,13 @@ wget ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/H
gzip -d GCA_000001405.15_GRCh38_full_analysis_set.fna.gz gzip -d GCA_000001405.15_GRCh38_full_analysis_set.fna.gz
mv GCA_000001405.15_GRCh38_full_analysis_set.fna hs38a.fa mv GCA_000001405.15_GRCh38_full_analysis_set.fna hs38a.fa
bwa index hs38a.fa bwa index hs38a.fa
cp bwa-hs38-res/hs38d4.fa.alt hs38a.fa.alt cp bwa-hs38-bundle/hs38d4.fa.alt hs38a.fa.alt
``` ```
Perform mapping: Perform mapping:
```sh ```sh
bwa mem hs38a.fa read1.fq read2.fq \ bwa mem hs38a.fa read1.fq read2.fq \
| bwa-hs38-res/k8-linux bwa-postalt.js hs38a.fa.alt \ | bwa-hs38-bundle/k8-linux bwa-postalt.js hs38a.fa.alt \
| samtools view -bS - > aln.unsrt.bam | samtools view -bS - > aln.unsrt.bam
``` ```
For short reads, the postprocessing script `bwa-postalt.js` runs at about the For short reads, the postprocessing script `bwa-postalt.js` runs at about the
@ -30,14 +30,14 @@ same speed as BAM compression.
Construct the index: Construct the index:
```sh ```sh
cat hs38a.fa bwa-hs38-res/hs38d4-extra.fa > hs38d4.fa cat hs38a.fa bwa-hs38-bundle/hs38d4-extra.fa > hs38d4.fa
bwa index hs38d4.fa bwa index hs38d4.fa
cp bwa-hs38-res/hs38d4.fa.alt . cp bwa-hs38-bundle/hs38d4.fa.alt .
``` ```
Perform mapping: Perform mapping:
```sh ```sh
bwa mem hs38d4.fa read1.fq read2.fq \ bwa mem hs38d4.fa read1.fq read2.fq \
| bwa-hs38-res/k8-linux bwa-postalt.js -p postinfo hs38d4.fa.alt \ | bwa-hs38-bundle/k8-linux bwa-postalt.js -p postinfo hs38d4.fa.alt \
| samtools view -bS - > aln.unsrt.bam | samtools view -bS - > aln.unsrt.bam
``` ```
This command line generates `postinfo.ctw` which loosely evaluates the presence This command line generates `postinfo.ctw` which loosely evaluates the presence