Can't progress Imputation for Chr X

[innerpyg-bi]

I analyzed by following steps.

1. docker run -d -p 4000 genepi/imputationserver:v1.2.7
2. access http://localhost:4000
3. install 1000genomes-phase3 reference panel in Admin Panel

• But There is no Chr X Reference data. So,

4. local download and make m3vcf and bcf files for Chr X
5. Insert the m3vcf and bcf file into /data/apps/1000g-phase-3-v5/2.0.0 on genepi/imputationserver:v1.2.7
6. docker exec -t -i ImputationServer cloudgene run [email protected] --files /mnt/$PWD/nonPAR.vcf.gz --refpanel apps@[email protected] --conf /etc/hadoop/conf --population eas &> docker.log

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In this case, I can see this log.

Please let me know how to fix
Thanks

[seppinho]

Can you try the same file on https://imputationserver.sph.umich.edu?

[innerpyg-bi]

Today, I analyzed web based imputation server using same file.
Chr22 vcf file was finished. but not ChrX.

[seppinho]

thanks for testing. any chances you can share a test file that fails?

[innerpyg-bi]

I'm sending you a vcf file with only the sample ID changed.
nonPAR_Update.vcf.gz

Thank you for your concern.

[seppinho]

Had to unzip/bgzip it again but worked then on the server. Can you please double check?
nonPAR_Update.vcf.gz

[innerpyg-bi]

Oh, i found when doesn't work on web.
When i select the reference panel which is EUR and Other/Mixed poputation of 1000G Phase3 V5 hg19, it works but not the others.
I also checked on docker, but still doesn't work including eur.

[o147942]

I cannot find the bcf file of the chrX in bcfs folder in hapmap and 1000g reference panel of docker.
Why there is no chrX file?