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fixed wrong FAQ links

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Heng Li 2014-05-14 14:36:52 -04:00
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README.md
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@ -62,10 +62,10 @@ do not have plan to submit it to a peer-reviewed journal in the near future.
2. [Why does a read appear multiple times in the output SAM?](#multihit) 2. [Why does a read appear multiple times in the output SAM?](#multihit)
3. [Does BWA work on reference sequences longer than 4GB in total?](#4gb) 3. [Does BWA work on reference sequences longer than 4GB in total?](#4gb)
4. [Why can one read in a pair has high mapping quality but the other has zero?](#pe0) 4. [Why can one read in a pair has high mapping quality but the other has zero?](#pe0)
5. [How can a BWA-backtrack alignment stands out of the end of a chromosome?](endref) 5. [How can a BWA-backtrack alignment stands out of the end of a chromosome?](#endref)
6. [How to map sequences to GRCh38 with ALT contigs?](#h38) 6. [How to map sequences to GRCh38 with ALT contigs?](#h38)
####<a href="type"></a>1. What types of data does BWA work with? ####<a name="type"></a>1. What types of data does BWA work with?
BWA works with a variety types of DNA sequence data, though the optimal BWA works with a variety types of DNA sequence data, though the optimal
algorithm and setting may vary. The following list gives the recommended algorithm and setting may vary. The following list gives the recommended
@ -103,7 +103,7 @@ errors given longer query sequences as the chance of missing all seeds is small.
As is shown above, with non-default settings, BWA-MEM works with PacBio subreads As is shown above, with non-default settings, BWA-MEM works with PacBio subreads
with a sequencing error rate as high as ~15%. with a sequencing error rate as high as ~15%.
####<a href="multihit"></a>2. Why does a read appear multiple times in the output SAM? ####<a name="multihit"></a>2. Why does a read appear multiple times in the output SAM?
BWA-SW and BWA-MEM perform local alignments. If there is a translocation, a gene BWA-SW and BWA-MEM perform local alignments. If there is a translocation, a gene
fusion or a long deletion, a read bridging the break point may have two hits, fusion or a long deletion, a read bridging the break point may have two hits,
@ -111,18 +111,18 @@ occupying two lines in the SAM output. With the default setting of BWA-MEM, one
and only one line is primary and is soft clipped; other lines are tagged with and only one line is primary and is soft clipped; other lines are tagged with
0x800 SAM flag (supplementary alignment) and are hard clipped. 0x800 SAM flag (supplementary alignment) and are hard clipped.
####<a href="4gb"></a>3. Does BWA work on reference sequences longer than 4GB in total? ####<a name="4gb"></a>3. Does BWA work on reference sequences longer than 4GB in total?
Yes. Since 0.6.x, all BWA algorithms work with a genome with total length over Yes. Since 0.6.x, all BWA algorithms work with a genome with total length over
4GB. However, individual chromosome should not be longer than 2GB. 4GB. However, individual chromosome should not be longer than 2GB.
####<a href="pe0"></a>4. Why can one read in a pair has high mapping quality but the other has zero? ####<a name="pe0"></a>4. Why can one read in a pair has high mapping quality but the other has zero?
This is correct. Mapping quality is assigned for individual read, not for a read This is correct. Mapping quality is assigned for individual read, not for a read
pair. It is possible that one read can be mapped unambiguously, but its mate pair. It is possible that one read can be mapped unambiguously, but its mate
falls in a tandem repeat and thus its accurate position cannot be determined. falls in a tandem repeat and thus its accurate position cannot be determined.
####<a href="endref"></a>5. How can a BWA-backtrack alignment stands out of the end of a chromosome? ####<a name="endref"></a>5. How can a BWA-backtrack alignment stands out of the end of a chromosome?
Internally BWA concatenates all reference sequences into one long sequence. A Internally BWA concatenates all reference sequences into one long sequence. A
read may be mapped to the junction of two adjacent reference sequences. In this read may be mapped to the junction of two adjacent reference sequences. In this
@ -130,7 +130,7 @@ case, BWA-backtrack will flag the read as unmapped (0x4), but you will see
position, CIGAR and all the tags. A similar issue may occur to BWA-SW alignment position, CIGAR and all the tags. A similar issue may occur to BWA-SW alignment
as well. BWA-MEM does not have this problem. as well. BWA-MEM does not have this problem.
####<a href="h38"></a>6. How to map sequences to GRCh38 with ALT contigs? ####<a name="h38"></a>6. How to map sequences to GRCh38 with ALT contigs?
BWA-backtrack and BWA-MEM partially support mapping to a reference containing BWA-backtrack and BWA-MEM partially support mapping to a reference containing
ALT contigs that represent alternative alleles highly divergent from the ALT contigs that represent alternative alleles highly divergent from the