Comments (3)
susannasiebert
commented on August 21, 2024
Hi Paul,
This appears to be a problem with some of your VCF entries, specifically the ORIGINAL_MUTECT_FILTER INFO field. This INFO field is defined like this:
##INFO=<ID=ORIGINAL_MUTECT_FILTER,Number=1,Type=String,Description="Original MuTect FILTER string">
i.e., a String field with exactly one value. However some of your VCF variants look like this
1 1560892 . C A . PASS BAFP=99;BAFP_NORMAL=9;ECNT=1;HCNT=36;MAD_LEFT_OFFSET=8.00;MAD_RIGHT_OFFSET=0.00;MAX_ED=.;MEDIAN_LEFT_OFFSET=12.00;MEDIAN_RIGHT_OFFSET=75.00;MIN_ED=.;NLOD=37.79;ORIGINAL_MUTECT_FILTER;TLOD=59.21;TLOD_FWD=23.42;TLOD_REV=35.80;TUMOR_SB_POWER_FWD=0.999;TUMOR_SB_POWER_REV=1.000;CSQ=A|intron_variant|MODIFIER|MIB2|ENSG00000197530|Transcript|ENST00000505820.2|protein_coding||7/19|ENST00000505820.2:c.1210-34C>A|||||||||1||HGNC|30577||||||MAGALRRGRALGSRPSGPTVSSRRSPQCPVAQEGLGARSRPRVAPRSLARCGPSSRLMGWKPSEARGQSQSFQASGLQPRSLKAARRATGRPDRSRAARPTMDPSAHRSRAAPPNMDPDPQAGVQVGMRVVRGVDWKWGQQDGGEGGVGTVVELGRHGSPSTPDRTVVVQWDQGTRTNYRAGYQGAHDLLLYDNAQIGVRHPNIICDCCKKHGLRGMRWKCRVCLDYDLCTQCYMHNKHELAHAFDRYETAHSRPVTLSPRQGLPRIPLRGIFQGAKVVRGPDWEWGSQDGGEGKPGRVVDIRGWDVETGRSVASVTWADGTTNVYRVGHKGKVDLKCVGEAAGGFYYKDHLPRLGKPAELQRRVSADSQPFQHGDKVKCLLDTDVLREMQEGHGGWNPRMAEFIGQTGTVHRITDRGDVRVQFNHETRWTFHPGALTKHHSFWVGDVVRVIGDLDTVKRLQAGHGEWTDDMAPALGRVGKVVKVFGDGNLRVAVAGQRWTFSPSCLVAYRPEEDANLDVAERARENKSSLSVALDKLRAQKSDPEHPGRLVVEVALGNAARALDLLRRRPEQVDTKNQGRTALQVAAYLGQVELIRLLLQARAGVDLPDDEGNTALHYAALGNQPEATRVLLSAGCRADAINSTQSTALHVAVQRGFLEVVRALCERGCDVNLPDAHSDTPLHSAISAGTGASGIVEVLTEVPNIDVTATNSQGFTLLHHASLKGHALAVRKILARARQLVDAKKEDGFTALHLAALNNHREVAQILIREGRCDVNVRNRKLQSPLHLAVQQAHVGLVPLLVDAGCSVNAEDEEGDTALHVALQRHQLLPLVADGAGGDPGPLQLLSRLQASGLPGSAELTVGAAVACFLALEGADVSYTNHRGRSPLDLAAEGRVLKALQGCAQRFRERQAGGGAAPGPRQTLGTPNTVTNLHVGAAPGPEAAECLVCSELALLVLFSPCQHRTVCEECARRMKKCIRCQVVVSKKLRPDGSEVASAAPAPGPPRQLVEELQSRYRQMEERITCPICIDSHIRLVFQCGHGACAPCGSALSACPICRQPIRDRIQIFV GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1 0/1:27,18:0.400:9:9:0.500:1099,657:14:13 0/0:127,0:0.00:0:0:.:5082,0:59:68
specifically, note how the ORIGINAL_MUTECT_FILTER is only ORIGINAL_MUTECT_FILTER;. This doesn't match the field definition. If it matched it would look like ORIGINAL_MUTECT_FILTER=some_filter;. I'm not sure what tool might be populating this field but I assume that variants like the above does not have a mutect filter set. In those cases this field should just be absent from the INFO fields.
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pjleo
commented on August 21, 2024
Dear Susan,
Thanks so much! I could not see the problem to save myself.
I replaced entries as you suggested and no problems.
Thanks again for getting back so quickly.
Cheers
Paul
FYI the entries were put in using a GATK walker. I think the error occurs when the filter is "." originally. So yes its a custom annotation that cased the problem
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susannasiebert
commented on August 21, 2024
You're welcome. I will be closing this ticket but do feel free to reopen should you run into any additional problems.
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Related Issues (20)
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