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Hello,

I'm using this helper function to prepare my input files for pVACtools. I don't see an error message but I'm pasting the output from my terminal below:

[W::vcf_parse] Extreme INFO/MPOS value encountered and set to missing at chr1:999089 Complex variant or MNP will be skipped: chr1 1053478 CC TT Complex variant or MNP will be skipped: chr1 1084023 GG AA Complex variant or MNP will be skipped: chr1 1286134 CC TT Complex variant or MNP will be skipped: chr1 1374278 GG AA Complex variant or MNP will be skipped: chr1 1512446 AA TT Complex variant or MNP will be skipped: chr1 1599654 CA TG Complex variant or MNP will be skipped: chr1 3631025 TC CT Complex variant or MNP will be skipped: chr1 3631034 AG GA Complex variant or MNP will be skipped: chr1 6128865 CC TT Complex variant or MNP will be skipped: chr1 6208979 CA TG

I am getting this same message for all the chromosomes. I checked my VCF file and I do have SNPs in the file. The 2 tsv files get created but are empty. Could you please advice on how to fix this ?

Thanks

At this time, trying to re-build the docker image fails due to pip being unable to install cyvcf2 properly. This is fixed in #1

I was trying to use this to count a large number of sites (~6 million potential germline SNP positions). Even with 10GB of memory requested my jobs were being killed due to exceeded memory usage.

I believe the issue is that it loads the whole ROI into memory before writing out the files needed by bam-readcount?

Hi is there any way at all to download this tool without using docker, as I do not have access to it through my departments server.