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Old 02-11-2013, 12:36 PM   #1
Location: UK

Join Date: Nov 2010
Posts: 49
Default Variant calling on custom amplicons with extremely high coverage

I have a hard time obtaining variants from a bam file constructed using amplicon sequencing. When I load bam's on IGV I can see loads of reads (well, there is a limit of how much You can really see but the depth show correct coverage). I have 30.000-1.500.000 reads (identical ones) per each bam file.
I tried to use GATK with specific region bed file (thought that it will speed it up) but it takes forever (already 5h+! for 6 regions of ~250bp).
Tried samtools mpileup (multiple bam's at once) but I cannot find any of known variants (visible under IGV).
Shall I use it one-by-one on each bam (and combine?)?
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