Question: GATK Interval list for processing mouse genome WGS
0
gravatar for husensofteng
20 months ago by
husensofteng130
Sweden
husensofteng130 wrote:

I am trying to apply the GATK best practices for calling variants but from mice WGS data. According to GATK, one of the reasons for using an interval list in processing WGS data is "to exclude regions that have bad or uninformative data where a tool is getting stuck”. GATK bundle includes such an interval list fo the human genome however I have not been able to find any interval list of “good” genomic regions for the mouse genome (GRCm38).

Also, since GATK does not provide information on the provenance of this file it is hard to replicate it for the mouse genome. I am looking for an interval list for GRCm38 or information on the source of the human interval file. Any help is highly appreciated.

wgs grcm38 gatk genome • 848 views
ADD COMMENTlink modified 4 months ago by igor9.9k • written 20 months ago by husensofteng130

Were you able to find this interval list?

ADD REPLYlink written 4 months ago by vctrm6710

Please use ADD COMMENT and not the answer field for comments.

ADD REPLYlink written 4 months ago by ATpoint32k
0
gravatar for igor
4 months ago by
igor9.9k
United States
igor9.9k wrote:

The calling regions file was generated using Picard IntervalListTools. The command is actually included in the file itself and described on the GATK support forum:

So it looks like it's taking the full genome, then removing the N bases (with no padding). The "call intervals" are the remaining good bases.

ADD COMMENTlink written 4 months ago by igor9.9k

If I'm not mistaken, this seems to require an interval list in the first place, which doesn't seem available for mouse

ADD REPLYlink written 4 months ago by vctrm6710
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