Question: hg19 interval list
0
gravatar for Nicolas Rosewick
4 months ago by
Belgium, Brussels
Nicolas Rosewick8.1k wrote:

Hi,

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

ftp://gsapubftp-anonymous@ftp.broadinstitute.org/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

hg19 interval gatk genome • 238 views
ADD COMMENTlink written 4 months ago by Nicolas Rosewick8.1k
1
gravatar for Nandini
4 months ago by
Nandini820
London
Nandini820 wrote:

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

ADD COMMENTlink written 4 months ago by Nandini820

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

ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by kianalee0
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