VCF QC By BamΒΆ

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.