I am trying to create a subset of 10k variants from 25-30 unmapped contigs of a g.vcf file including the header

Question

My objective is to take a g.vcf.gz file and from 25-30 unmapped contigs with titles like "NW_020192317.1", I want to make a subset of ~10k variants from each of the unmapped contigs and make one final g.vcf file that includes the header from the original g.vcf.gz file.

From the post here, I have tried running:

samtools view -bo output.g.vcf -s 123.4 inputfile.g.vcf.gz NW_020192317.1

and I keep receiving the output:

Aborted (core dumped)

I'm not too picky about the number of variants per contig, as long as it is in the thousands, that's why I tried using ".4"

Alternatively, I tried using the code:

samtools view input.g.vcf.gz "NW_020192317.1:1-2" > output.g.vcf

and I recieved the same response of "Aborted (core dumped)" with nothing else. I am confused what is wrong here and why it is throwing an error.

Answer 1

After some guidance from my advisor, this command allowed me to get the output file I needed.

bcftools view -o newvcfFileName.g.vcf -s 123.2 locationOfTheFile chrom1 chrom2 ... chrom23(mito DNA) --force-samples

I listed every chromosome's title until I typed --force-samples. I found it simpler to copy and paste the names in.