Notice:
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

Lots of nulls in MV file

Hi, i'm tying to find variants in a trio. I just read a thread where Laurent mentioned an overflow giving a -1 value in the MendelianViolations file. I have lots of these. Can anyone clarify what this means? Is it that the coverage is too high to bother counting e.g. over 250 or something like that. I notice the -1 is associated with a null TP score. Is this because the TP score is based on the DP values? Also associated with -GT ./. -AD . -PL . It looks like a lot of info is missing ie these blanks are DO have reads. I'm worried the variants are called using a value of zero for one idividual.....

How do I handle these variants? are they real?

Cheers, Rob

Top of file...... CHROM POS AC FAMILY TP MOTHER_GT MOTHER_DP MOTHER_AD MOTHER_PL FATHER_GT FATHER_DP FATHER_AD FATHER_PL CHILD_GT CHILD_DP CHILD_AD CHILD_PL 1 13302 4 Day null ./. -1 . . C|C 87 37,54 0,42,883 T|C 213 0,213 65,9,0 1 91190 7 Day null ./. -1 . . A|G 16 5,11 246,0,60 A|A 14 1,13 364,5,0 1 91336 7 Day null ./. -1 . . T|A 26 11,16 368,0,75 T|T 27 9,19 512,21,0 1 91354 10 Day null ./. -1 . . A|A 32 10,23 576,3,0 A|A 30 9,22 644,36,0 1 136733 1 Day 2 G/G 87 81,10 0,99,1878 G/G 237 194,55 0,169,5127 G/T 238 182,68 80,0,4936 1 136751 1 Day 16 A/A 93 83,13 0,97,1909 A/A 238 184,61 0,106,4077 A/G 238 165,82 280,0,3990 1 714427 38 Day null ./. -1 . . A|A 6 0,6 185,18,0 A|A 8 0,8 225,21,0 1 761957 4 Day null ./. -1 . . AT|AT 7 0,6 243,18,0 AT|AT 8 0,7 330,21,0 1 787185 10 Day 2 A|A 3 0,3 33,3,0 ./. -1 . . A|A 5 0,5 33,3,0 1 789050 4 Day 2 A|A 18 9,9 32,3,0 ./. -1 . . A|A 19 6,13 32,3,0 1 854978 34 Day null ./. -1 . . C|C 1 0,1 34,3,0 C|C 7 0,7 220,21,0 1 870129 6 Day null ./. -1 . . C|C 1 0,1 22,3,0 C|C 1 0,1 23,3,0 1 870169 8 Day null ./. -1 . . G|G 1 1,0 0,3,22 T|G 1 0,1 23,3,0

Answers

  • LaurentLaurent Member, Broadie ✭✭

    Hi FGPonce,

    Thanks for posting this! Indeed, there were some problems with overflows giving -1 values for the TP. However in your case, it does not look like this is the problem. I'm actually really puzzled about what is going on since it seems like PBT is reporting what doesn't seem like MendelianViolations at all. Clearly it is linked to one individual being problematic since there is always one of the parent's genotype missing. Normally when the genotype is ./. (with other fields as '.' or '-1', it means that there is no genotype called in the original VCF.

    In any case, would you mind posting (or sending me) the original VCF file for first couple of sites reported here? Can you also specify all options you're using and the ped file.

    Thanks!
    Laurent

Sign In or Register to comment.