Hi,
Is it possible that depth is different between a VCF file and a CRAM file? When I uploaded two files to IGV software and clicked the information track box shown by the VCF file and the coverage track box shown by the CRAM file, I found that their depth is different, as shown in the attached image. I greatly appreciate your help.
In all of these cases, the depths refer not to the depth of the original file but to the depth of the alignments that were considered and contributed to the genotyping.
For example, to me, it looks like the first alignment in the image also has two deletions very close by, so that alignment is a whole lot less trustworthy. Some of the bases around the deletion also seems to have low qualities (the color is faded, I think that is what it means).
I believe the variant caller ignored that alignment when making the variant determination and in the end used only 6 alignments out of the possible 7.
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version 2.3.6
Guess you forgot to attach the image. You can edit the post above and add that.
IGV may down sample data when displaying it so make sure you have turned that setting off in preferences.
Hi,
Thank you for answering, and I have tried to follow your instruction to turn the downsampling off in preference, but they are still different. I would like to inquire whether it could happen to the results. I greatly appreciate your help.
Who made the VCF file? samtools also will downsample during genotype calling. In this case, I see it reports allele depths of 4 and 2, and I see 5 and 2 on IGV. so one of them was not counted. Maybe identical reads are dismissed, genotypers dont like to reuse identical reads, but IGV will show them.
can you show us that line in the VCF:
cat PC_1-7.wf_snp_clinvar.vcf | grep 69078931