pb
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Latest activity by pb-
pb commented,
Hi Anthony DiCi, Oh I see, thanks a lot for looking into it! All is clear from my side Best, Patricia
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pb created a post,
GATK HaplotypeCaller issues with Genotyping (GT)
Hello, I am using GATK v4.2.6.1. I am working on a haploid organism. Previously described in - HaplotypeCaller calls 0/0 when all reads in raw BAM support 1/1 – GATK (broadinstitute.org) -I am also...
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pb commented,
Hi Anthony, Thank you very much for the swift response from your side. I ran the CountReads on my BAM file and this was the output (see below). From this documentations, WellformedReadFilter – G...
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pb created a post,
Haploytpe caller shows me that 0 read(s) were filtered by: MappingQualityAvailableReadFilter etc.
AnsweredHello, I am using GATK v4.2.6.1. I am working on a haploid organism. However, I noticed the following program log: 19:19:24.445 INFO HaplotypeCaller - 638650 read(s) filtered by: MappingQualityRea...