I am in the process of using PSMC to look at my populations demographic history, but I am having issues with the conversion from fastq to psmcfa.
I followed the recommendations as best as I could on the github page (https://github.com/lh3/psmc), though I did my variant call with the entire cohort rather than one individual as they show. After the variant call, I extract the variants for each of my samples and filter for Q>20, and then convert to fastq using 'vcfutils.pl vcf2fq'.
All goes well, and my consensus fastq seems correct, though I have only lost a small portion (less than 1%) of my variants in the filter which seems a bit relaxed, but it's what they suggest. When I use PSMC's fq2psmcfa module though, the resulting file is 0 bytes, and thus completely blank inside. I used the following code;
utils/fq2psmcfa -q20 whole_genome_indivdual1.fq > whole_genome_individual1.psmcfa
Unfortunately, PSMC doesn't throw out any error messages, and I've tried with a smaller file size and unfiltered fastq files, but nothing happens.
Anybody have any ideas what is going wrong? I'm tempted to run the variant call once again just in case there was a mistake somewhere earlier in the pipeline I missed.