{"action":"created","issue":{"url":"https://api.github.com/repos/samtools/bcftools/issues/501","repository_url":"https://api.github.com/repos/samtools/bcftools","labels_url":"https://api.github.com/repos/samtools/bcftools/issues/501/labels{/name}","comments_url":"https://api.github.com/repos/samtools/bcftools/issues/501/comments","events_url":"https://api.github.com/repos/samtools/bcftools/issues/501/events","html_url":"https://github.com/samtools/bcftools/issues/501","id":184477817,"number":501,"title":"gVCF homozygous blocks","user":{"login":"Jhermes22","id":22980200,"avatar_url":"https://avatars.githubusercontent.com/u/22980200?v=3","gravatar_id":"","url":"https://api.github.com/users/Jhermes22","html_url":"https://github.com/Jhermes22","followers_url":"https://api.github.com/users/Jhermes22/followers","following_url":"https://api.github.com/users/Jhermes22/following{/other_user}","gists_url":"https://api.github.com/users/Jhermes22/gists{/gist_id}","starred_url":"https://api.github.com/users/Jhermes22/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Jhermes22/subscriptions","organizations_url":"https://api.github.com/users/Jhermes22/orgs","repos_url":"https://api.github.com/users/Jhermes22/repos","events_url":"https://api.github.com/users/Jhermes22/events{/privacy}","received_events_url":"https://api.github.com/users/Jhermes22/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":3,"created_at":"2016-10-21T12:54:39Z","updated_at":"2016-11-04T22:01:17Z","closed_at":null,"body":"Hi,\n\nI am getting conflicting calls for some positions in my vcf file, with the same site being marked both as SNP and part of a homozygous block.\n\nAn example of my vcf file:\n\ncontig86    436259  .   C   A   228 PASS    DP=46;VDB=4.76112e-09;SGB=-0.693146;RPB=0.666667;MQB=0.178571;MQSB=0.999927;BQB=0.0238095;MQ0F=0;AC=2;AN=2;DP4=2,0,25,17;MQ=55  GT:PL:DP:SP:DP4 1/1:255,80,0:44:3:2,0,25,17\ncontig86    436259  .   c   .   .   PASS    END=436313  GT  0/0\n\nThis is the command used to obtain the vcf.\n\nsamtools mpileup -q 20 -Q 20 -ugt DP,SP,DP4 -f reference.fas -r contig86 bamfile.bam \\\n | bcftools call -m -O v -g 8 \\\n | bcftools filter -sFILTER -g3 -G10 -e'%QUAL<20 || FMT/DP<8' - > test.vcf\n\nThis is the output from samtools mpileup, before bcftools.\n\ncontig86    436257  .   G   <X> 0   .   DP=49;I16=27,16,0,0,1640,63560,0,0,2401,138103,0,0,865,20267,0,0;QS=1,0;MQSB=0.997163;MQ0F=0    PL:DP:SP:DP4    0,129,255:43:0:27,16,0,0\ncontig86    436258  .   T   <X> 0   .   DP=46;I16=27,18,0,0,1751,68863,0,0,2483,142187,0,0,909,21143,0,0;QS=1,0;MQSB=0.948756;MQ0F=0    PL:DP:SP:DP4    0,135,255:45:0:27,18,0,0\ncontig86    436259  .   C   A,<X>   0   .   DP=46;I16=2,0,25,17,54,1458,1653,65495,79,3121,2382,138582,35,725,877,20567;QS=0.0323935,0.967606,0;VDB=4.76112e-09;SGB=-0.693146;RPB=0.666667;MQB=0.178571;MQSB=0.999927;BQB=0.0238095;MQ0F=0  PL:DP:SP:DP4    255,80,0,255,126,255:44:3:2,0,25,17\ncontig86    436259  .   catctcgggtaatctcgggtaatctcgggtaatctcg   cATCTCGGGTAATCTCGGGTAatctcgggtaatctcgggtaatctcgggtaatctcg   0   .   INDEL;IDV=1;IMF=0.0217391;DP=46;I16=20,16,1,0,6891,1.42137e+06,255,65025,2088,122724,39,1521,826,19744,25,625;QS=0.981578,0.0184223;VDB=1.48144e-09;SGB=-0.379885;MQSB=0.998122;MQ0F=0  PL:DP:SP:DP4    0,72,255:37:0:20,16,1,0\ncontig86    436260  .   A   <X> 0   .   DP=53;I16=28,23,0,0,1907,73193,0,0,2864,165866,0,0,987,22425,0,0;QS=1,0;MQSB=0.965492;MQ0F=0    PL:DP:SP:DP4    0,154,255:51:0:28,23,0,0\ncontig86    436261  .   T   <X> 0   .   DP=53;I16=27,22,0,0,1909,75255,0,0,2782,161782,0,0,981,22487,0,0;QS=1,0;MQSB=0.999546;MQ0F=0    PL:DP:SP:DP4    0,148,255:49:0:27,22,0,0\n\nProbably the indel is causing the confusion, but this does not seem right? How do I avoid having the same site being called variable and homozygous-reference in the vcf?\n\nThanks!\n"},"comment":{"url":"https://api.github.com/repos/samtools/bcftools/issues/comments/258558495","html_url":"https://github.com/samtools/bcftools/issues/501#issuecomment-258558495","issue_url":"https://api.github.com/repos/samtools/bcftools/issues/501","id":258558495,"user":{"login":"pd3","id":524074,"avatar_url":"https://avatars.githubusercontent.com/u/524074?v=3","gravatar_id":"","url":"https://api.github.com/users/pd3","html_url":"https://github.com/pd3","followers_url":"https://api.github.com/users/pd3/followers","following_url":"https://api.github.com/users/pd3/following{/other_user}","gists_url":"https://api.github.com/users/pd3/gists{/gist_id}","starred_url":"https://api.github.com/users/pd3/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pd3/subscriptions","organizations_url":"https://api.github.com/users/pd3/orgs","repos_url":"https://api.github.com/users/pd3/repos","events_url":"https://api.github.com/users/pd3/events{/privacy}","received_events_url":"https://api.github.com/users/pd3/received_events","type":"User","site_admin":false},"created_at":"2016-11-04T22:01:16Z","updated_at":"2016-11-04T22:01:16Z","body":"Any chance you could share the few output lines directly from `mpileup`? Although not impossible, it is more difficult to debug the problem going backwards, from the outputs. Thanks"}}
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