Hello All,
I have a bam file generated by MiSeq + GATK (Realignment/recalibration), I use samtools (v0.1.18) / GATK for variant calling. For a site, I find a big difference about the depth between these two methods.
bcftools view sample.bcf | awk '$1=="chr7" && $2==150648198'
chr7 150648198 . A G,X 0 . DP=8;I16=1,0,0,1,24,576,25,625,60,3600,60,3600,25,625,25,625;VDB=0.0000 PLP:SP 19,0,18,22,21,40:2:0
Here DP=8 before quality control and only two reads passed quality control, thus samtools does not call variant for this site.
GATK with default setting calls this site as SNP with DP=516, and IGV shows there are 233A + 283G at this site with good quality (mapQ~37, baseQ~30.
This site is a true SNP confirmed by Sanger sequencing, so any explanation will be appreciated.
Many thanks!
I have a bam file generated by MiSeq + GATK (Realignment/recalibration), I use samtools (v0.1.18) / GATK for variant calling. For a site, I find a big difference about the depth between these two methods.
bcftools view sample.bcf | awk '$1=="chr7" && $2==150648198'
chr7 150648198 . A G,X 0 . DP=8;I16=1,0,0,1,24,576,25,625,60,3600,60,3600,25,625,25,625;VDB=0.0000 PLP:SP 19,0,18,22,21,40:2:0
Here DP=8 before quality control and only two reads passed quality control, thus samtools does not call variant for this site.
GATK with default setting calls this site as SNP with DP=516, and IGV shows there are 233A + 283G at this site with good quality (mapQ~37, baseQ~30.
This site is a true SNP confirmed by Sanger sequencing, so any explanation will be appreciated.
Many thanks!
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