Are there plans to release a new version which can use the newer versions of samtools (i.e., 1.x instead of 0.1.x)?
If anyone is having issues with nan's and zero estimates in their .psmc files (pik, \sum{l\not=k}A{kl}, A{kk}), make sure to use the older 0.1.x versions of samtools/bcftools to generate the fq.gz input. Samtools 0.1.19 includes bcftools view which is used to call variants (as opposed to bcftools call in standalone bcftools verisons). The commands will not work if you mix old and new versions of samtools/bcftools.
EDIT: Alright, just so everyone knows, changing all my versions of samtools did NOT result in a success. Still trying to figure out where in my pipeline I'm going wrong.
EDIT II: So it turns out I was calling the .psmcfa file from the wrong location. The program will not crash if you call a nonexistent file, it will just read it as empty, causing nan's. I am now trying to use the most recent samtools and bcftools to call variants and generate the diploid.fq.gz file. Will update when pipeline is finished running.
EDIT III: Using versions SAMtools/1.9-GCC-7.4.0 and BCFtools/1.9-GCC-7.4.0 resulted in successful psmc plots both singly and by bootstrapping.
Are there plans to release a new version which can use the newer versions of samtools (i.e., 1.x instead of 0.1.x)?
If anyone is having issues with nan's and zero estimates in their .psmc files (pik, \sum{l\not=k}A{kl}, A{kk}), make sure to use the older 0.1.x versions of samtools/bcftools to generate the fq.gz input. Samtools 0.1.19 includes
bcftools viewwhich is used to call variants (as opposed tobcftools callin standalone bcftools verisons). The commands will not work if you mix old and new versions of samtools/bcftools.EDIT: Alright, just so everyone knows, changing all my versions of samtools did NOT result in a success. Still trying to figure out where in my pipeline I'm going wrong.
EDIT II: So it turns out I was calling the .psmcfa file from the wrong location. The program will not crash if you call a nonexistent file, it will just read it as empty, causing nan's. I am now trying to use the most recent samtools and bcftools to call variants and generate the diploid.fq.gz file. Will update when pipeline is finished running.
EDIT III: Using versions SAMtools/1.9-GCC-7.4.0 and BCFtools/1.9-GCC-7.4.0 resulted in successful psmc plots both singly and by bootstrapping.
Good luck to everyone running PSMC analysis!