Hello,
I am trying to use the --LROH option in vcftools, but am struggling with how to use the --chr flag when my vcf file is in scaffold notation instead of chromosome notation.
I am trying to run this for loop:
for i in {alaudinus, beldingi, brooksi, nevadensis, rostratus} do for f in { } do
vcftools --gzvcf /project/sedmands_1143/ekirsch/savannahsparrow/savannahsparrow/41-Passerculus/41-Passerculus/41-Passerculus_final.vcf.gz --LROH --chr"$f" --keep "$i"_list.txt --out /project/sedmands_1143/ekirsch/savannahsparrow/savannahsparrow/41-Passerculus/41-Passerculus/"$i"_Chr"$f"
done done
My VCF file has 337 different contig names formatted like "JAKOOL010000001.1".
Can I provide the --chr flag with a .txt file with a list of all of these contig names? If so, how would I include this in the for loop? Or if there is a simpler way to do this I am open to any other options!
Thank you so much in advance! I am pretty new to bioinformatics and this is my first time trying to calculate ROH so any guidance is appreciated.
