HaplotypeCallerΒΆ

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