diff --git a/README.md b/README.md index dff245e..be4bc99 100644 --- a/README.md +++ b/README.md @@ -130,38 +130,6 @@ 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 as well. BWA-MEM does not have this problem. -####6. How to map sequences to GRCh38 with ALT contigs? - -BWA-backtrack and BWA-MEM partially support mapping to a reference containing -ALT contigs that represent alternative alleles highly divergent from the -reference genome. - - # download the K8 executable required by bwa-helper.js - wget http://sourceforge.net/projects/lh3/files/k8/k8-0.2.1.tar.bz2/download - tar -jxf k8-0.2.1.tar.bz2 - - # download the ALT-to-GRCh38 alignment in the SAM format - wget http://sourceforge.net/projects/bio-bwa/files/hs38.alt.sam.gz/download - - # download the GRCh38 sequences with ALT contigs - wget ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Homo_sapiens/GRCh38/seqs_for_alignment_pipelines/GCA_000001405.15_GRCh38_full_analysis_set.fna.gz - - # index and mapping - bwa index -p hs38a GCA_000001405.15_GRCh38_full_analysis_set.fna.gz - bwa mem -h50 hs38a reads.fq | ./k8-linux bwa-helper.js genalt hs38.alt.sam.gz > out.sam - -Here, option `-h50` asks bwa-mem to output multiple hits in the XA tag if the -read has 50 or fewer hits. For each SAM line containing the XA tag, -`bwa-helper.js genalt` decodes the alignments in the XA tag, groups hits lifted -to the same chromosomal region, adjusts mapping quality and outputs all the -hits overlapping the reported hit. A read may be mapped to both the primary -assembly and one or more ALT contigs all with high mapping quality. - -Note that this procedure assumes reads are single-end and may miss hits to -highly repetitive regions as these hits will not be reported with option -`-h50`. `bwa-helper.js` is a prototype implementation not recommended for -production uses. - [1]: http://en.wikipedia.org/wiki/GNU_General_Public_License