Dear community,
I'm interested in analysing Whole genome GraphTyper joint call pVCF and I'm wondering if there is a readme explaining, for each chromosome, the number of files for that chromosome and the points of break. And, in affirmative case, where is it possible to find it.
I have this question because I see that the vcf files available at the following path '/Bulk/Whole genome sequences/Whole genome GraphTyper joint call' are divided by chromosome chunks. However, we have different files with '_c9_' , for example, and having a document explaining how many breaks we have per chromosome and in which point would be really useful.
At the moment, I found a readme that describes the vcf file information and qc metrics but this file does not include this specific information (attached).
Thank you in advance for your support,
Veronica
The file qc_metrics_graphtyper_v2.7.1_qc.tab.gz located in QC folder would have the column "contig" and "POS" for the variants that you need and the "region" column indicating which region those variants belong to. You can use that information to figure out which files among those files you need.
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The file qc_metrics_graphtyper_v2.7.1_qc.tab.gz located in QC folder would have the column "contig" and "POS" for the variants that you need and the "region" column indicating which region those variants belong to. You can use that information to figure out which files among those files you need.
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