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DiagnoseTargets NO_READS flagged where there are reads
In my diagnose targets output I have a lot of NO_READS, but most of the targets are ones that have a SNP called by HC on the same set of bam files:
# # # table(rowData(nextseq.dt.vcf)$FILTER) # # # LOW_COVERAGE LOW_COVERAGE;NO_READS NO_READS # # # 2136 1114 14775 # # # NO_READS;POOR_QUALITY PASS POOR_QUALITY # # # 307 56599 479
I have had a look at one site that is flagged as NO_READS, but there are reads:
line from unfiltered VCF from HC
chr1 109808776 . C G 106.25 . AC=1;AF=0.042;AN=24;BaseQRankSum=-1.059e+00;ClippingRankSum=-2.329e+00;DP=127;FS=0.000;GQ_MEAN=36.25;GQ_STDDEV=35.51;InbreedingCoeff=-0.0565;MLEAC=1;MLEAF=0.042;MQ=52.57;MQ0=0;MQRankSum=1.48;NCC=0;QD=6.64;ReadPosRankSum=-2.120e-01 GT:AD:DP:GQ:PL 0/0:4,0:4:12:0,12,87 0/0:12,0:12:36:0,36,297 0/0:7,0:7:21:0,21,169 0/0:21,0:21:60:0,60,514 0/0:8,0:8:24:0,24,172 0/0:6,0:6:6:0,6,90 0/0:11,0:11:24:0,24,254 0/0:11,0:11:27:0,27,288 0/0:11,0:11:27:0,27,255 0/1:9,7:16:99:141,0,1720/0:11,0:11:30:0,30,321 0/0:9,0:9:27:0,27,228
line from DiagnoseTargets
chr1 109808776 . C <DT> . NO_READS END=109808776;GC=1.00;IDP=165.00 FT:IDP:LL:ZL NO_READS:6.00:0:0 NO_READS:20.00:0:0 NO_READS:11.00:0:0 NO_READS:22.00:0:0 NO_READS:10.00:0:0 NO_READS:11.00:0:0 NO_READS:14.00:0:0 PASS:13.00:0:0 NO_READS:9.00:0:0 PASS:15.00:0:0 PASS:19.00:0:0 NO_READS:15.00:0:0
Is there any other filters that these reads are not passing - I couldn't spot anything in the documentation but I wouldn't put it past me!
I ran a fairly standard incantation of DiagnoseTargets, I did use --interval_merging OVERLAPPING_ONLY though.