useful tools, but could it be used for hg19 or other genome build?

[lxsbch]

Hi,

this is really good tool, but can it be used to process bam file map to hg19 or other build except GRCH？
Do you recommend what to do, if we have bam in hg19?

thanks in advance

[drmjc]

Hi, thanks for your message. We are refactoring the code to add x38 support, and in so doing will add functionality for hg19 'chr1' style contig names. ETA is about 2 months. All the best, Mark

…

On Sat, 4 Dec 2021, 12:36 pm lxsbch, ***@***.***> wrote: Hi, this is really good tool, but can it be used to process bam file map to hg19 or other build except GRCH？ Do you recommend what to do, if we have bam in hg19? thanks in advance — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#17>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAEQQM3SZUCX4IW3MWXXBJDUPFWCRANCNFSM5JK7IYPA> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

[lxsbch]

thanks for your reply

Hi, thanks for your message. We are refactoring the code to add x38 support, and in so doing will add functionality for hg19 'chr1' style contig names. ETA is about 2 months. All the best, Mark
…
On Sat, 4 Dec 2021, 12:36 pm lxsbch, @.***> wrote: Hi, this is really good tool, but can it be used to process bam file map to hg19 or other build except GRCH？ Do you recommend what to do, if we have bam in hg19? thanks in advance — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#17>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAEQQM3SZUCX4IW3MWXXBJDUPFWCRANCNFSM5JK7IYPA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

best,
Shirley

[katkaciska]

Hello, I would like to ask whether there were any updates on the possibility of using hg19 as the genome of reference?
Thank you in advance!

Katarina

[drmjc]

Hi, x38 support is now in, so we're testing hg19 next. The main refactoring thread is here #13

[Yixiangzhang1996]

Can it be used as a reference for genome construction in any species and then analyzed?