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SVs in some chromosomes are missing in nr_deletion files #44
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Hi Anson,
Thank you for pointing out this error in our NR data. We have identified the problem in our pipeline and are working on a fix. Please check back occasionally until the data are restored.
Thanks,
Tim
=============================
Timothy Hefferon, Ph.D.
Staff Scientist, Human Variation
National Center for Biotechnology Information
45 Center Dr., Rm. 5AN.36D-14
Bethesda, MD 20892-6512, USA
(301) 496-5884
***@***.******@***.***>
=============================
On Aug 9, 2022, at 2:40 AM, Anson Wong ***@***.******@***.***>> wrote:
Hello,
I downloaded the latest version of all files in the directory /pub/dbVar/sandbox/sv_datasets/nonredundant/deletions.
However, it seems the SVs in chr 1, chr2, chr11, chr12 and X are missing in some files (e.g. GRCh37.nr_deletions.tsv, GRCh37.nr_deletions.bed, GRCh37.nr_deletions.tsv, and GRCh38.nr_deletions.bed).
For example, when I checked the file using sed '1,2d' GRCh38.nr_deletions.tsv | cut -f1 | sort -k1,1V | uniq -c, it gives:
183462 3 215779 4 179941 5 186375 6 177445 7 156126 8 100796 13 102341 14 88040 15 103951 16 97261 17 84456 18 89493 19 73053 20 46757 21 51888 22 7323 Y 56 mt
But GRCh38.nr_deletions.pathogenic.tsv (which I believe is a subset of GRCh38.nr_deletions.tsv) seemed to contain SVs from all chromosomes:
sed '1,2d' GRCh38.nr_deletions.pathogenic.tsv | cut -f1 | sort -k1,1V | uniq -c
1126 1 1657 2 788 3 499 4 677 5 729 6 863 7 561 8 725 9 452 10 691 11 370 12 409 13 321 14 765 15 1415 16 1175 17 342 18 489 19 272 20 189 21 661 22 1847 X 76 Y 16 mt
Would be great if you could help update the files. Thank you!
Best,
Anson
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It's been almost 2 years but it appears this hasn't been fixed 😢. Downloaded the files from this site but the deletions tsv and bed files are still missing those chromosomes. @thefferon How's the fix coming along? |
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Hello,
I downloaded the latest version of all files in the directory
/pub/dbVar/sandbox/sv_datasets/nonredundant/deletions
.However, it seems the SVs in chr 1, 2, 9, 10, 11, 12 and X are missing in some files (e.g. GRCh37.nr_deletions.tsv, GRCh37.nr_deletions.bed, GRCh37.nr_deletions.tsv, and GRCh38.nr_deletions.bed).
For example, when I checked the file using
sed '1,2d' GRCh38.nr_deletions.tsv | cut -f1 | sort -k1,1V | uniq -c
, it gives:183462 3
215779 4
179941 5
186375 6
177445 7
156126 8
100796 13
102341 14
88040 15
103951 16
97261 17
84456 18
89493 19
73053 20
46757 21
51888 22
7323 Y
56 mt
But GRCh38.nr_deletions.pathogenic.tsv (which I believe is a subset of GRCh38.nr_deletions.tsv) contains SVs from all chromosomes:
sed '1,2d' GRCh38.nr_deletions.pathogenic.tsv | cut -f1 | sort -k1,1V | uniq -c
1126 1
1657 2
788 3
499 4
677 5
729 6
863 7
561 8
725 9
452 10
691 11
370 12
409 13
321 14
765 15
1415 16
1175 17
342 18
489 19
272 20
189 21
661 22
1847 X
76 Y
16 mt
Would be great if you could help update the files. Thank you!
Best,
Anson
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