hg19 interval list

Question

[Nicolas Rosewick]

Hi,

In GATK's resource bundle, there is an interval list for hg38 for scatter-gather purposes.

ftp://[e-mail]/bundle/hg38/wgs_calling_regions.hg38.interval_list

Quick view of the file :

chr1    10001   207666  +   . intersection ACGTmer
chr1    257667  297968  +   . intersection ACGTmer
chr1    347969  535988  +   . intersection ACGTmer
chr1    585989  2702781 +   . intersection ACGTmer
chr1    2746291 12954384    +   . intersection ACGTmer
chr1    13004385    16799163    +   . intersection ACGTmer
chr1    16849164    29552233    +   . intersection ACGTmer
chr1    29553836    121976459   +   . intersection ACGTmer
chr1    122026460   124977944   +   . intersection ACGTmer
chr1    124978327   125130246   +   . intersection ACGTmer
chr1    125131848   125171347   +   . intersection ACGTmer

Is there a similar one for hg19 ?

Thank you

[LauferVA]

i would try UCSC table browser for this. almost certainly have something similar.

Answer 1

[Isam]

In case anyone is still looking for this, as of 2022 the hg19 WGS is obtainable here

If that's no longer up, try searching for the filename wgs_calling_regions.v1.interval_list with the keyword hg19.

Answer 2

[NB]

maybe not on the gatk bundle site. But probably a liftover should work ?

[kianalee]

I tried doing this by first making the resources_broad_hg38_v0_wgs_calling_regions.hg38.interval_list

into a BED file.

sed 's/:\|-/\t/gi' resources_broad_hg38_v0_wgs_calling_regions.hg38.interval_list > resources_broad_hg38_v0_wgs_calling_regions.hg38.bed

And using this as the input for the UCSC liftover tool.

But UCSC gave the following error:

ERROR: Unsupported data format