detect MNP variants using by Haplotypecaller

zhuwenjuanzhuwenjuan chinaPosts: 5Member


I used Haplotypecaller 3.1 to detect MNP variants.
java -Xmx6g$PWD -jar $GATK -R $hg19 -T HaplotypeCaller -I $bamlist --dbsnp $dpsnp135 -o $call/$sample.all.vcf -stand_call_conf 50.0 -stand_emit_conf 10.0 -dcov 200 -nct $nct -A SpanningDeletions -A TandemRepeatAnnotator -A HomopolymerRun -A AlleleBalance -l INFO -baqGOP 30 --max_alternate_alleles 2 -rf BadCigar --minPruning 5

The result had no MNP type varaints, but I can find some continuous snp variants. these snp variants didn't be combined to MNP variants.
Is this normal ? or I really didn't get MNP variants ?

Best Answer


  • SheilaSheila Broad InstitutePosts: 2,390Member, GATK Dev, Broadie, Moderator, DSDE Dev admin


    Hi. Please post an IGV screenshot of the region and the relevant lines from the VCF file so we can determine what is going on.



  • zhuwenjuanzhuwenjuan chinaPosts: 5Member
    edited April 2014

    @Sheila‌ the problem is that none of MNp variants were detected by GATK 3.1. Thanks

    Post edited by zhuwenjuan on
  • zhuwenjuanzhuwenjuan chinaPosts: 5Member
    edited April 2014

    Part of my result:

    1 12987327 rs142575927 G A 762.77 dbSNP AC=2;AF=1.00;AN=2;DB;DP=27;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=25.77;MQ0=0;QD=28.25 GT:AD
    :GQ:PL 1/1:0,27:81:791,81,0

    1 12987349 . G A 1605.77 PASS AC=2;AF=1.00;AN=2;DP=36;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=28.17;MQ0=0;QD=27.93 GT:AD:GQ:PL

    1 12987350 . A T 1605.77 PASS AC=2;AF=1.00;AN=2;DP=37;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=28.04;MQ0=0;QD=33.89 GT:AD:GQ:PL

    1 12987602 rs76625528 T C 797.77 dbSNP AC=2;AF=1.00;AN=2;DB;DP=28;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=28.24;MQ0=0;QD=28.49 GT:AD:GQ:PL 1/1:0,28:84:826,84,0

    It looks like I can't upload the IGV picture. this MNP has high quality.

    Post edited by zhuwenjuan on
  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 8,737Administrator, GATK Dev admin

    Just to be clear -- what you're expecting is for positions 1:12987349 and 1:12987350 to be emitted together as a MNP with alleles GA/AT, correct?

    Geraldine Van der Auwera, PhD

  • zhuwenjuanzhuwenjuan chinaPosts: 5Member

    yes, 1:12987349 and 1:12987350 , now just continuous snp variants ,not combine together. If I care about MNP, I cann't directly extract this variants.

Sign In or Register to comment.