Number of variants in each vcf file

General
1

Hi all,
in order to validate our postprocessing of gnomad vcf files for all releases (v2.1.1, v3.1.2, v4.1.0) it would be extremely helpful to have a table with the number of variants in each original vcf file. Of course I can count the number of non-header lines myself but as the files are huge and on cloud storage this is a matter of days :see_no_evil:
I did the task for v4.1.0 genomes but would be very happy if I don’t need to do it for the other versions/cohorts

chr1    59160006
chr2    62931878
chr3    51235008
chr4    50142330
chr5    46410785
chr6    43703160
chr7    42466679
chr8    39939308
chr9    33833698
chr10   35497598
chr11   35080671
chr12   34332175
chr13   24993777
chr14   23568672
chr15   22225848
chr16   24719921
chr17   21944455
chr18   19467717
chr19   17293274
chr20   16355695
chr21   10958898
chr22   11608143
chrX    30297561
chrY    1169063

Thanks!
Max

2

Hi Max,

Here are the variant counts for each version. We also recommend verifying that the MD5 hashes match those listed on the downloads page after downloading the files.

chromosome v2_genomes v2_exomes v3_genomes v4_genomes v4_exomes
1 20370890 1707147 59159991 59160006 17671166
2 21892245 1230614 62929395 62931878 12963790
3 17834355 958850 51232827 51235008 10208076
4 17423639 642129 50144242 50142330 7252480
5 16290654 740678 46413277 46410785 8156768
6 15190442 835212 43702087 43703160 8573431
7 14752321 845891 42467077 42466679 9233607
8 14073574 621220 39937920 39939308 6800081
9 11480614 713431 33830205 33833698 7476742
10 12118750 665745 35496856 35497598 7210142
11 12345492 1044543 35078200 35080671 10526962
12 11933435 889014 34331057 34332175 9855795
13 8693573 287655 24993787 24993777 3549140
14 8220638 589647 23566763 23568672 6268134
15 7723667 611216 22224163 22225848 7010578
16 8618657 866022 24716971 24719921 8785928
17 7373819 1031902 21943471 21944455 10744750
18 6893751 253290 19466619 19467717 3246732
19 5991870 1231680 17290209 17293274 11706291
20 5516836 429586 16354200 16355695 4616729
21 3483000 187702 10958207 10958898 2188842
22 3567085 416866 11606640 11608143 4845199
X 10153029 403070 30290736 30297561 4685140
Y NA 6862 1167367 1169063 140758

Regards,
Kristen

1 Like
3

this is great, thank you so much! :clap: