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Old 06-29-2015, 10:39 PM   #2
Location: Uppsala, Sweden

Join Date: Mar 2010
Posts: 23

Hello Daniele,

To at least partly answer your question: HaplotypeCaller performs local realignment within the run, so your "final bam file" is actually not the one you input to HaplotypeCaller but something you don't see.. So HC might realign a region and find an indel, while in your input bam you see nothing or one ore more SNPs (which likely is caused by mismatches in an anyway wrong alignment).

If you want to see how it looks like AFTER HaplotypeCaller has realigned the reads, you can rerun it using the flag:
--bamOutput newbamfile.bam
(takes quite a while to run).

You can also make it print out all possible haplotypes to the bam with:
and then see them in IGV (choose "color alignment by: tag" and then write "HC" in the box).

Hope this helps at least a bit,
Linnea is offline   Reply With Quote