VCF QC By Bam
With aligned reads and a suitable VCF file we can now inspect the results.
$ mkdir -p vcfqcbybam_output_dir
$ pbrun vcfqcbybam \
--ref parabricks_sample/Ref/Homo_sapiens_assembly38.fasta \
--in-vcf variants.vcf \
--in-bam output.bam \
--out-file vcfqcbybam_pileup.txt \
--output-dir vcfqcbybam_output_dir
Please visit https://docs.nvidia.com/clara/#parabricks for detailed documentation
conda 4.10.3
------------------------------------------------------------------------------
|| Parabricks accelerated Genomics Pipeline ||
|| Version 3.7 ||
|| samtoolsmpileup ||
|| Contact: Parabricks-Support@nvidia.com ||
------------------------------------------------------------------------------
[14:21:28] chr-1:-1
[14:21:29] chr0:32285000
[14:21:30] chr0:87694000
[14:21:31] chr0:152306000
[14:21:32] chr0:204460000
[14:21:33] chr1:14344000
[14:21:34] chr1:62418000
[14:21:35] chr1:130814000
[14:21:36] chr1:189854000
[14:21:37] chr2:4295000
[14:21:38] chr2:49684000
[14:21:39] chr2:122740000
[14:21:40] chr2:179333000
[14:21:41] chr3:46724000
[14:21:42] chr3:110179000
[14:21:43] chr3:178491000
[14:21:44] chr4:52922000
[14:21:45] chr4:119197000
[14:21:46] chr4:172006000
[14:21:47] chr5:43781000
[14:21:48] chr5:116060000
[14:21:49] chr5:161347000
[14:21:50] chr6:62142000
[14:21:51] chr6:106462000
[14:21:52] chr7:3053000
[14:21:53] chr7:56166000
[14:21:54] chr7:124490000
[14:21:55] chr8:32634000
[14:21:56] chr8:114276000
[14:21:57] chr9:30532000
[14:21:58] chr9:86517000
[14:21:59] chr10:3702000
[14:22:00] chr10:65613000
[14:22:01] chr10:115477000
[14:22:02] chr11:30547000
[14:22:03] chr11:80171000
[14:22:04] chr12:26111000
[14:22:05] chr12:101722000
[14:22:06] chr13:62670000
[14:22:07] chr14:41669000
[14:22:08] chr14:98939000
[14:22:09] chr15:53287000
[14:22:10] chr16:9479000
[14:22:11] chr16:48070000
[14:22:12] chr17:8666000
[14:22:13] chr18:104000
[14:22:14] chr18:38611000
[14:22:15] chr19:32436000
[14:22:16] chr20:14005000
[14:22:17] chr21:45344000
[14:22:18] chr22:95343000
[14:22:19] chr261:783000
------------------------------------------------------------------------------
|| Program: samtoolsmpileup ||
|| Version: 3.7 ||
|| Start Time: Fri Sep 24 14:21:19 2021 ||
|| End Time: Fri Sep 24 14:22:20 2021 ||
|| Total Time: 1 minute 1 second ||
------------------------------------------------------------------------------
------------------------------------------------------------------------------
|| Parabricks accelerated Genomics Pipeline ||
|| Version 3.7 ||
|| readsampileup ||
|| Contact: Parabricks-Support@nvidia.com ||
------------------------------------------------------------------------------
------------------------------------------------------------------------------
|| Program: readsampileup ||
|| Version: 3.7 ||
|| Start Time: Fri Sep 24 14:22:21 2021 ||
|| End Time: Fri Sep 24 14:24:26 2021 ||
|| Total Time: 2 minutes 5 seconds ||
------------------------------------------------------------------------------
vcfqcbybam completed
You should now have the following files:
$ 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
-rw-r--r-- 1 root root 23161024401 Sep 24 14:22 vcfqcbybam_pileup.txt
-rw-r--r-- 1 root root 18893 Sep 24 14:24 vcfqcbybam_pileup.summary.csv
drwxr-xr-x 3 root root 4096 Sep 24 14:24 vcfqcbybam_output_dir
If you open vcfqcbybam_output_dir/bamqc_report.html in a browser, you'll see a
page similar to the following. You can pan and zoom each image using the
controls to the right of each image. The 'circling lines' icon (third from the
bottom) resets the pan and zoom.
Clara Parabricks VCF QC
VCF File Name:
A histogram of the number of variants within a window of 1000 basepairs. Note, empty windows are not included in this plot.