[W::vcf_parse] Extreme INFO/MPOS value encountered and set to missing at chr1:17082839

[jeongmeani]

Hi, Happy new year!

i ran bcftools to parse tumor sample of somatic vcf.
but it returned warning message like below

[W::vcf_parse] Extreme INFO/MPOS value encountered and set to missing at chr1:17082839

my code is
bcftools view -s TNB_17_tumor TNB_17.mutect2.filtered.vcf.gz > TNB_17.mutect.tumor.vcf

i have a look input vcf and out vcf file but i don't know what is difference among them
and even at chr1:17082839 the line is same!

what is the problem?

Thanks!

[pd3]

Can you show the value of INFO/MPOS at that position before and after? Also, important, what version of htslib+bcftools are you running? Make sure to test with 1.10.2 or the latest github version.

[jeongmeani]

OK!

before

chr1 165378737 . C T . PASS CONTQ=93;DP=99;ECNT=1;GERMQ=93;MBQ=38,35;MFRL=228,228;MMQ=60,60;MPOS=-2147483648;NALOD=1.44;NLOD=7.51;POPAF=6.00;SEQQ=18;STRANDQ=17;TLOD=7.18 GT:AD:AF:DP:F1R2:F2R1:SB 0/0:26,0:0.036:26:10,0:15,0:22,4,0,0 0/1:57,4:0.083:61:25,3:29,0:44,13,3,1

after

chr1 165378737 . C T . PASS CONTQ=93;DP=99;ECNT=1;GERMQ=93;MBQ=38,35;MFRL=228,228;MMQ=60,60;MPOS=.;NALOD=1.44;NLOD=7.51;POPAF=6;SEQQ=18;STRANDQ=17;TLOD=7.18;AC=1;AN=2 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:57,4:0.083:61:25,3:29,0:44,13,3,1

i think this is perfectly match each other.
and my version is 1.10.2.

[pd3]

The error message and your data are consistent and quite clear: MPOS=-2147483648 was out of bounds and is replaced by MPOS=.

[jkbonfield]

Note this is caused by a bug in Mutect2. More information and background here:

https://gatkforums.broadinstitute.org/gatk/discussion/24398/mpos-is-2147483648-in-mutect2-gatk-4-1-3-0

broadinstitute/gatk#5492

samtools/htslib#999

The change in bcftools / htslib is that with extra validation it is not spotted these illegal values and issuing a warning. Older versions just truncated or wrapped around the data silently.

[jeongmeani]

OK!
i got it.
Thank you for your answers.

happy new year!

Jeongmin.