WHAMG analysis runs with Illumina DRAGEN 3.7.6 cram output producing empty VCF files

[Solyris83]

Hi, as said in the topic. We are testing WHAMG on 1KGP OpenAccess data which has been reprocessed with DRAGEN 3.7.6 found in
https://aws.amazon.com/blogs/industries/dragen-reanalysis-of-the-1000-genomes-dataset-now-available-on-the-registry-of-open-data/

We tested on 63 samples with the Docker image which is created for the WHAMG module in the NF-Core modules repo
quay.io/biocontainers/mulled-v2-fb3127231a8f88daa68d5eb0eec49593cd98b440:e6a1c182ebdfe372b5e3cdc05a6cece64cef7274-0

Command runs are found below

prefix='sample1'
fasta='hg38'
whamg -f ${cram} -a ${fasta} | bgzip --stdout > ${prefix}.vcf.gz
tabix ${prefix}.vcf.gz

The output ${prefix}.vcf.gz is an empty file. The (nextflow) process did not error out.

Please do advise if WHAM is compatible with DRAGEN (or dragmap which is the underlying aligner) ?

[zeeev]

I don't think there is cram support.