HaplotypeCaller
Now that you have a BAM file, you can convert it to a VCF file.
$ pbrun haplotypecaller \
--ref parabricks_sample/Ref/Homo_sapiens_assembly38.fasta \
--in-bam output.bam \
--out-variants variants.vcf
Please visit https://docs.nvidia.com/clara/#parabricks for detailed documentation
------------------------------------------------------------------------------
|| Parabricks accelerated Genomics Pipeline ||
|| Version 3.6.1-1.beta6 ||
|| GPU-GATK4 HaplotypeCaller ||
|| Contact: Parabricks-Support@nvidia.com ||
------------------------------------------------------------------------------
[PB Info 2021-Sep-24 14:10:55] 0 /mnt/dsk/output.bam/mnt/dsk/variants.vcf
[PB Info 2021-Sep-24 14:10:55] ProgressMeter - Current-Locus Elapsed-Minutes Regions-Processed Regions/Minute
[PB Info 2021-Sep-24 14:11:05] chr1:54647917 0.2 245608 1473648
[PB Info 2021-Sep-24 14:11:15] chr1:155356779 0.3 593719 1781157
[PB Info 2021-Sep-24 14:11:25] chr1:237988754 0.5 958094 1916188
[PB Info 2021-Sep-24 14:11:35] chr2:70214289 0.7 1310890 1966335
[PB Info 2021-Sep-24 14:11:45] chr2:178233496 0.8 1764217 2117060
[PB Info 2021-Sep-24 14:11:55] chr3:20428770 1.0 2136917 2136917
[PB Info 2021-Sep-24 14:12:05] chr3:115628316 1.2 2543754 2180358
[PB Info 2021-Sep-24 14:12:15] chr4:2025558 1.3 2910235 2182676
[PB Info 2021-Sep-24 14:12:25] chr4:107995024 1.5 3360630 2240420
[PB Info 2021-Sep-24 14:12:35] chr5:16026380 1.7 3784607 2270762
[PB Info 2021-Sep-24 14:12:45] chr5:123503845 1.8 4226070 2305129
[PB Info 2021-Sep-24 14:12:55] chr6:16541468 2.0 4556047 2278021
[PB Info 2021-Sep-24 14:13:05] chr6:134586901 2.2 5037206 2324862
[PB Info 2021-Sep-24 14:13:15] chr7:39650655 2.3 5371069 2301884
[PB Info 2021-Sep-24 14:13:25] chr7:132148744 2.5 5760930 2304372
[PB Info 2021-Sep-24 14:13:35] chr8:54734144 2.7 6101334 2288000
[PB Info 2021-Sep-24 14:13:45] chr9:9187004 2.8 6532435 2305565
[PB Info 2021-Sep-24 14:13:55] chr9:117681313 3.0 6911680 2303893
[PB Info 2021-Sep-24 14:14:05] chr10:75893671 3.2 7334488 2316153
[PB Info 2021-Sep-24 14:14:15] chr11:23246185 3.3 7694416 2308324
[PB Info 2021-Sep-24 14:14:25] chr11:117595132 3.5 8094548 2312728
[PB Info 2021-Sep-24 14:14:35] chr12:54167743 3.7 8399201 2290691
[PB Info 2021-Sep-24 14:14:45] chr13:22631898 3.8 8772011 2288350
[PB Info 2021-Sep-24 14:14:55] chr13:110841538 4.0 9157276 2289318
[PB Info 2021-Sep-24 14:15:05] chr14:96004751 4.2 9507052 2281692
[PB Info 2021-Sep-24 14:15:15] chr15:97713421 4.3 9874655 2278766
[PB Info 2021-Sep-24 14:15:25] chr16:88934373 4.5 10234951 2274433
[PB Info 2021-Sep-24 14:15:35] chr17:51235132 4.7 10435708 2236222
[PB Info 2021-Sep-24 14:15:45] chr18:38838331 4.8 10729120 2219817
[PB Info 2021-Sep-24 14:15:55] chr19:40492545 5.0 11080414 2216082
[PB Info 2021-Sep-24 14:16:05] chr20:52622112 5.2 11385272 2203601
[PB Info 2021-Sep-24 14:16:15] chr22:17059188 5.3 11609202 2176725
[PB Info 2021-Sep-24 14:16:25] chrX:75206147 5.5 12035237 2188224
[PB Info 2021-Sep-24 14:16:36] Total time taken: 340.962824
-----------------------------------------------------------
|| Program: GPU-GATK4 HaplotypeCaller ||
|| Version: 3.6.1-1.beta6 ||
|| Start Time: Fri Sep 24 14:10:39 2021 ||
|| End Time: Fri Sep 24 14:16:36 2021 ||
|| Total Time: 5 minutes 57 seconds ||
------------------------------------------------------------------------------
You should now have the following files in your directory:
$ ls -lrt
-rw-r--r-- 1 root root 4728919831 Sep 24 14:09 output.bam
-rw-r--r-- 1 root root 6882792 Sep 24 14:09 output.bam.bai
-rw-r--r-- 1 root root 87690 Sep 24 14:09 output_chrs.txt
-rw-r--r-- 1 root root 23567904 Sep 24 14:16 variants.vcf
(sample data not shown)
The first ten non-header lines of variants.vcf should be as follows:
chr1 16378 . T C 45.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=23.55;QD=22.64;SOR=2.303 GT:AD:DP:GQ:PL 1/1:0,2:2:6:57,6,0
chr1 63268 . T C 43.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=23.09;QD=21.64;SOR=2.303 GT:AD:DP:GQ:PL 1/1:0,2:2:6:55,6,0
chr1 63516 . A G 1202.03 . AC=2;AF=1.00;AN=2;DP=40;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=26.22;QD=30.05;SOR=1.292 GT:AD:DP:GQ:PL 1/1:0,40:40:99:1216,120,0
chr1 63527 . T C 1002.03 . AC=2;AF=1.00;AN=2;DP=33;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=26.05;QD=30.36;SOR=1.179 GT:AD:DP:GQ:PL 1/1:0,33:33:99:1016,99,0
chr1 131609 . C A 83.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.275;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=20.00;MQRankSum=0.000;QD=7.60;ReadPosRankSum=-1.349;SOR=0.551 GT:AD:DP:GQ:PL 0/1:6,5:11:91:91,0,115
chr1 133483 . G T 70.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.534;DP=8;ExcessHet=3.0103;FS=3.332;MLEAC=1;MLEAF=0.500;MQ=26.65;MQRankSum=1.611;QD=8.83;ReadPosRankSum=-0.703;SOR=2.303 GT:AD:DP:GQ:PL 0/1:5,3:8:78:78,0,100
chr1 264627 . A G 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=49.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0
chr1 268012 . G A 330.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.636;DP=116;ExcessHet=3.0103;FS=1.639;MLEAC=1;MLEAF=0.500;MQ=39.33;MQRankSum=-6.168;QD=2.85;ReadPosRankSum=-1.358;SOR=0.895 GT:AD:DP:GQ:PL 0/1:93,23:116:99:338,0,3307
chr1 268130 . G T 2188.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.543;DP=228;ExcessHet=3.0103;FS=8.632;MLEAC=1;MLEAF=0.500;MQ=44.88;MQRankSum=-12.533;QD=9.60;ReadPosRankSum=1.105;SOR=0.356 GT:AD:DP:GQ:PL 0/1:128,100:228:99:2196,0,4482
chr1 268516 . C T 59.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.465;DP=7;ExcessHet=3.0103;FS=3.680;MLEAC=1;MLEAF=0.500;MQ=52.18;MQRankSum=-0.180;QD=8.51;ReadPosRankSum=-0.366;SOR=2.258 GT:AD:DP:GQ:PL 0/1:5,2:7:67:67,0,138