Regarding GenotypeGVCFs

tanu06tanu06 CanadaMember

Hi,
This question may be not relevant but i could find answer to my question so thought of posting it,
I have been running Haplotyper and CombineGVCFs followed by GenotypeGVCFs but there is drastic change in number of SNPs in file which i get after GenotypeGVCFs , any suggestion or readings for the same.

With regards,
Tanushree

Best Answer

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin
    Can you please clarify if you are seeing a big difference in SNPs specifically, or in number of vcf records overall? If it is the latter I would suggest reading the documentation that explains what is a GVCF and how it's different from a vcf.
  • tanu06tanu06 CanadaMember

    Hi,
    Thank you so much for your quick response and sorry for bothering, I ran haplotyper with gvcf option followed by comineGVCf and GenotypeGVCF, but GenotypeGVCFs gives me bit odd results. I. One of them is below :

    GenotypeGVCFs file

    CHROM POS ID REF ALT QUAL FILTER INFO FORMAT S2 S4 S5 S6 S7 S8 S9

    1.1 44368 . G GA 240.30 . AC=2;AF=1.00;AN=2;DP=552;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=10.22;QD=20.03;SOR=1.473 GT:AD:DP:GQ:PL 1/1:0,12:15:45:238,45,0 ./.:86,0:86 ./.:79,0:79 ./.:80,0:80 ./.:78,0:78 ./.:111,0:111 ./.:102,0:102

    CombineGVCF file

    CHROM POS ID REF ALT QUAL FILTER INFO FORMAT S2 S4 S5 S6 S7 S8 S9

    1.1 44368 . G GA,GAA, . . DP=552;ExcessHet=3.01;RAW_MQ=57600.00 GT:AD:DP:GQ:MIN_DP:PL:SB ./.:0,12,3,0:15:0:.:238,45,0,146,0,121,187,34,130,164:0,0,5,10 ./.:.:87:0:86:0,0,0,0,0,0,0,0,0,0 ./.:.:81:0:79:0,0,0,0,0,0,0,0,0,0 ./.:.:80:0:80:0,0,0,0,0,0,0,0,0,0 ./.:.:80:0:78:0,0,0,0,0,0,0,0,0,0 ./.:.:112:0:111:0,0,0,0,0,0,0,0,0,0 ./.:.:106:0:102:0,0,0,0,0,0,0,0,0,0

    Secondly ./. specifies missing or same as reference allele.

    Thanking you in anticipation
    With regards,
    Tanushree Tiwari

  • tanu06tanu06 CanadaMember

    Hi,
    Thank you for your quick response, what about S2 sample where combinegVCF had ./. whereas GenotypeGVCFs file has 1/1.

    With regards,
    Tanushree

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin
    It looks like the joint calling ruled out the other alt alleles as being insufficiently plausible. That eliminated the uncertainty and enabled the caller to make a more confident call.
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