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szpiech / selscan

Haplotype based scans for selection
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EHH physical position instead of locus ID #126

Open cymdp opened 2 days ago

cymdp commented 2 days ago

Hello,

I'm trying to get EHH values in a 20kb window around a certain locus. I'm analyzing the X chromosome, but after quality control, the label is 23 instead of X. I have a map file containing the correct information. However, for my X chromosome iHS output files, all of my locus ID positions are output as "." I don't have this issue with the autosome output files.

Nonetheless, I still got the results I needed with the missing locus IDs for iHS. But EHH requires a locus ID or physical position. With the locus ID option not working for me due to the map file, I decided to try the physical position option for the --ehh flag. But I keep getting this error message:

selscan v2.0.3 ERROR: Must specify one and only one of EHH (--ehh) iHS (--ihs) XP-EHH (--xpehh) PI (--pi) nSL (--nsl) XP-nSL (--xpnsl) iHH12 (--ihh12)

and this is an example of the command I'm using:

Run selscan for EHH with additional options

selscan --ehh 154528523 --vcf chrX_males_qc_fixed.vcf --map males_chrX.map --out ss_ehh_males_chrX --ehh-win 20000

I was wondering if you have any tips for what I'm doing wrong, and how I can go about getting EHH values with selscan?

Thanks in advance!

szpiech commented 19 hours ago

Hello,

Sorry for this, looks like I fixed this in 2.0.3a but I haven't pushed it to main branch. Which OS are you using? I have macos-arm available currently. If you're using linux I'll have to get one compiled for you.

Zachary

On Mon, Sep 16, 2024 at 4:14 PM cymdp @.***> wrote:

Hello,

I'm trying to get EHH values in a 20kb window around a certain locus. I'm analyzing the X chromosome, but after quality control, the label is 23 instead of X. I have a map file containing the correct information. However, for my X chromosome iHS output files, all of my locus ID positions are output as "." I don't have this issue with the autosome output files.

Nonetheless, I still got the results I needed with the missing locus IDs for iHS. But EHH requires a locus ID or physical position. With the locus ID option not working for me due to the map file, I decided to try the physical position option for the --ehh flag. But I keep getting this error message:

selscan v2.0.3 ERROR: Must specify one and only one of EHH (--ehh) iHS (--ihs) XP-EHH (--xpehh) PI (--pi) nSL (--nsl) XP-nSL (--xpnsl) iHH12 (--ihh12)

and this is an example of the command I'm using: Run selscan for EHH with additional options

selscan --ehh 154528523 --vcf chrX_males_qc_fixed.vcf --map males_chrX.map --out ss_ehh_males_chrX --ehh-win 20000

I was wondering if you have any tips for what I'm doing wrong, and how I can go about getting EHH values with selscan?

Thanks in advance!

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cymdp commented 19 hours ago

Okay, great!

I'm using Linux on my university's cluster, so once you have this version publicly available I'll have to contact IT and get them to download the module.