psmc
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Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model
Hello, Thank you for this super useful tool. I was able to run it successfully. However, I have a question regarding choosing the optimum `-t `value and `-p` model. I...
Hi team - Have been trying out some different parameters for the -N, -t, and -p flags (based on published materials), but I'm having a hard time interpreting the differences...
Hello, I’d like to ask whether `psmc` is supported on Linux/Mac ARM64 systems ? Any concerns ? Any positive/negative experience ? Thank you!
Hi all, I have successfully ran my psmc for a few species, the regular run works out fine with no errors. and now I am running the bootstrapping segment of...
Hello again team. I am generating PSMC plots for multiple species, and I keep seeing, across most of them, sudden increases in Ne that shoot into >1e06. Occasionally the plots...
I have two independently produced plots for two related species and would like to combine them onto a single set of axes for comparison. I see this in multiple manuscripts...
I am running the following code: ``` samtools mpileup -uf ref.fasta sorted.bam | bcftools call -c | vcfutils.pl vcf2fq | gzip > Cmar.fq.gz psmc/utils/fq2psmcfa -q20 Cmar.fq.gz > Cmar.psmcfa psmc/psmc -N25...
Hi! I am trying to use psmc, and it seems to work fine (i.e. without rising errors) up to the plotting part. I always get the same error: ``` Use...
The pipeline to generate the input for psmc has always been `samtools mpileup -C50 -uf ref.fa aln.bam | bcftools view -c - | vcfutils.pl vcf2fq -d 10 -D 100 |...
Hi ! when i running PSMC , I met this error in step "psmc -N25 -t15 -r5 -p "4+25*2+4+6" -o diploid.psmc diploid.psmcfa seq 100 | xargs -i echo psmc -N25...
