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Old 10-24-2017, 02:53 PM   #1
peterlchang
Junior Member
 
Location: Los Angeles

Join Date: Mar 2010
Posts: 5
Cool SNPs at Interval Boundaries in GATK HaplotypeCaller

I'm using HaplotypeCaller with the -L option, where I explicitly state the interval. I am trying to break my task into pieces and assign it to different jobs for it to complete faster. In one run, I am running it, from say,

Chr1:1-1000000

and another run, I am running it twice, from

Chr1:1-500000 on one jobs and
Chr1:500001-1000000 on another

essentially splitting the interval into 2 different jobs. What I am seeing in this second run is that there are SNPs identified +/- 100 bases from 500000 that are not found in the first run.

My guess is that asking HC to focus only on a region (ie -L 1-500000) does not allow the local aligner to reassemble properly the reads, and hence results in spurious reads and SNPs. I was hoping that by specifying -L, it does the local aligner in a larger region and just report the SNPs in the -L region.

Has anybody heard of this or have a way around?
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gatk, haplotypecaller, interval, snp calling

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