Irantzu
Irantzu
Hello! I have noticed for the first time that sometimes Strelka2 gives to GT field a value of 1. See the following VCF record: `chr1 5553 . A G 78...
Hi there! I'm testing speedseq somatic utility and I have just seen the following variant in the output VCF file: `10 131751295 . TAAAAAAAAAAAAAAAGAAGAAGAAGAAGAAAGAAAGAAAAGAAAGAAGAAAGACAGAAAAAAAAATCT TAAAAAAAAAAAAAAGAAGAAGAAGAAGAAAGAAAGAAAAGAAAGAAGAAAGACAGAAAAAAAAATCT,TAAAAAAAAAAAAAAAAGAAGAAGAAGAAGAAAGAAAGAAAAGAAAGAAGAAAGACAGAAAAAAAAATCT 0.229037 PASS SSC=28.2554;AB=0,0;ABP=0,0;AC=0,0;AF=0,0;AN=2;AO=1,1;CIGAR=1M1D67M,1M1I68M;DP=2;DPB=42.2899;DPRA=0,0;EPP=5.18177,5.18177;EPPR=0;GTI=0;LEN=1,1;MEANALT=2,2;MQM=60,60;MQMR=0;NS=1;NUMALT=2;ODDS=2.91792;PAIRED=1,1;PAIREDR=0;PAO=12.3333,12.8333;PQA=429.667,451.667;PQR=517.667;PRO=14.8333;QA=29,32;QR=0;RO=0;RPL=0,0;RPP=5.18177,5.18177;RPPR=0;RPR=1,1;RUN=1,1;SAF=0,1;SAP=5.18177,5.18177;SAR=1,0;SRF=0;SRP=0;SRR=0;TYPE=del,ins;technology.illumina=1,1 GT:GQ:DP:RO:QR:AO:QA:GL 0/0:12.8928:2:0:0:1,1:29,32:0,-28.2554,-0.364147,-30.5296,-31.0235,-3.06672...
Hi there! I'm trying to make a somatic simulation. First, I have simulated germline data as suggested: `python varsim.py --vc_in_vcf All.vcf.gz --reference hs37d5.fa --sv_insert_seq insert_seq.txt --sv_dgv GRCh37_hg19_supportingvariants_2013-07-23.txt --id simu --read_length...
Hi there! I have recently started using open-cravat (oc), and I have noticed some annotations missing when using pharmgkb. For example, for variant `rs1803274`, when using oc I get the...
Hi! Is it possible to use HRC reference panel for imputation? Would it be possible for imputation to create reference panel that includes not only 1kG data but also Haplotype...
I have a general question about AD\* counters. For some cases I get 2 counters, for other 3, or 4... look at the following example. For the first variant 3...