Hi,

I'm trying to concatenate and then sort a set of gVCF files.
The particular set of gVCF.gz files sum to 17GB.

After the following concatenation operation

bcftools \
    concat \
    --naive \
    -f all_raw_vcfs.txt \
    --output-type v \
    -o concatedated_raw.vcf

The following sort command keeps getting killed

bcftools \
    sort \
    -m ${work_memory}G \
    --temp-dir tm_sort \
    --output-type z \
    -o ${prefix}.vcf.gz \
    concatedated_raw.vcf

Even when the machine has 600GB of memory.

So I am wondering

• what am I doing wrong?
• what memory footprint should be expected based on input file size?

Thanks!
Steve

bcftools version 1.13, compiled from source.