Variants of QUAL 0 have FILTER Value of PASS

[DarioS]

I am exploring Mity output. What do these mean?

chrM    383     .       T       A,G     0       PASS
chrM    385     .       A       C       0       PASS
chrM    387     .       C       A       1.80    SBA
chrM    391     .       T       A       0       PASS
chrM    394     .       C       A       10.10   PASS

There should perhaps be a couple of sentences explaining it added to the user guide.

[drmjc]

Hi Dario,
Thanks for reporting this issue. It's not one I've noticed, so can you provide a reproducible example?

[DarioS]

Commands are in the header section. See lines beginning with ##freebayesCommandline and ##mityCommandline of test.txt. File extenstion renamed from vcf to txt to allow upload to GitHub, but it's really a VCF file. Only QUAL 0 and PASS shown.

[drmjc]

I see a couple of things that could cause this. First I think you've supplied a cram, which mity doesn't officially support and second I see three samples in the VCF file - do you have three different samples within the same CRAM?

…

On Mon, 14 Mar 2022 at 17:00, Dario Strbenac ***@***.***> wrote: Commands are in the header section. See lines beginning with ##freebayesCommandline and ##mityCommandline of test.txt <https://github.com/KCCG/mity/files/8241982/test.txt>. File extenstion renamed from vcf to txt to allow upload to GitHub, but it's really a VCF file. Only QUAL 0 and PASS shown. . — Reply to this email directly, view it on GitHub <#13 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAEQQM2S4RGWWVMDGPYANS3U73IW7ANCNFSM5QEZLWAQ> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you commented.Message ID: ***@***.***>

[DarioS]

Yes, input was CRAM format. The Garvan Institute core facility found BAM and CRAM format produced the same output in testing and applies mity to CRAM files as part of their production pipeline. No, each sample is in one VCF. They use GATK's CombineVariants, according to the header:

##GATKCommandLine.CombineVariants ... [(RodBinding name=variant source=11_21_PK6_Clone2.mity.vcf.gz), (RodBinding name=variant2 source=11_21_PK6_Clone4.mity.vcf.gz), (RodBinding name=variant3 source=11_21_PK6_Fibro.mity.vcf.gz)])] out=/paella/CRAMPipeline/projects/RYADAV/R_211102_RYADAV_DNA_M001/mity/work/4c/2e9edf3447194cdb12b0c3321ceb3a/R_211102_RYADAV_DNA_M001.mity.vcf.gz ...