rwk-unil / xsqueezeit Goto Github PK

You need to change ubuntu base image from 21.04 to 20.04 which is LTS

Alternatively, if you use the last version of ubuntu, you cannot compile htslib with this message:
configure: error: cannot find required auxiliary files: config.guess config.sub

Hi,

We are testing xsqueezeit to compress and quickly access variant data from a large WGS cohort. The data structure concept is cool, and we liked it so far in our tests. We especially like how it makes variant annotation and INFO parsing blazing fast by decoupling the huge GT matrix from the rest of the variant data.

However, as described in the docs, the main limitation is that only GT information is stored at the moment.

Would it be possible in the future to allow the user to select which other format fields to include from the source VCF? This can be more flexible than adding a pre-selected list of importable FORMAT fields through issues/requests. Also, it is not easy to know in advance which fields one would like to import as variant callers, etc. evolve.

In general, for us at the moment, this can be a minimum list of FORMAT fields that we need to have included if we want to adopt xsqueezeit in our workflow:

• for imputed VCF data: DS:HDS:GP
• for other VCF data: GQ:DP:AD:GP

However, as said, it would be great if these fields could be configured when performing compression.

Thanks!

Hello, I discovered that variants outside my region of interest were sometimes included in my output. Is there a way to prevent this, other than filtering again with bcftools?

xsqueezeit -x -f chr20.xsi -r "20:614471-657881" | bcftools query -f '%ID,%POS\n'

0              20-614465-CTCTCTCTCTA-C,614465
1        20-614467-CTCTCTCTATATA-CTATA,614467
2          20-614467-CTCTCTCTATATA-CTA,614467
3            20-614467-CTCTCTCTATATA-C,614467
4      20-614469-CTCTCTATATATA-CTATATA,614469
...                                       ...
10004                    20-657856-C-T,657856
10005                    20-657864-T-G,657864
10006                    20-657871-T-C,657871
10007                    20-657879-A-G,657879
10008                    20-657881-A-G,657881