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iontorrent / TS

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TMAP do not get the header right when realigning bam #31

Open lituan opened 7 years ago

lituan commented 7 years ago

I used tmap map4 to realign a aligned bam to another reference fasta, found that tmap will keep original @SQ header and just append new reference. But tmap does not consider original @SQ header when it assigns the reference id, so when I used samtools to view the new realigned bam, I found many reads's reference are the orignal ones. For example, if original @SQ has ['chr1', 'chr2'], and new reference has ['chr3', chr4'], then a read which maps to 'chr3' will be assigned reference id 0 and get 'chr1' as reference.

Tato14 commented 6 years ago

Could you please post an example of TMAP commnad line? Thanks!