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lh3 / psmc

Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model
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Erroneous Result（Straight line） #7

Open YingLi13 opened 6 years ago

YingLi13 commented 6 years ago

Hi， I used the same command line for analyze of more than 30 individuals，More than half of them got erroneous result（straight line），just like the figure.While the other individuals got relatively reasonable result but the effective population size of them was increase to infinity at recent time as shown in figure. image

image

And my command as follows： 1） samtools mpileup -d 150 -q 20 -Q 20 -l Ref.non.repeat.bed.gz -uf Ref.fa individual.bam | bcftools view -c - | vcfutils.pl vcf2fq | gzip - > cns.fq.gz 2） psmc/utils/ fq2psmcfa -q20 cns.fq.gz > diploid.psmcfa 3） psmc/utils/splitfa diploid.psmcfa > split.fa 4） psmc/psmc -N25 -t15 -r5 -p \"4+25*2+4+6\" -o $outdir/diploid.psmc diploid.psmcfa

Why do some individuals on the same command line have no result? How to correct my procedure?

Looking forward to your reply.Thanks!

northloki commented 4 years ago

Hi, I also have the same problem, and the coverage of sequencing data > 18 X. I don't know why. Have you solved this problem? Thanks!

sjfleck commented 4 years ago

From my experience, lower -t15 to -t10 and run all of your samples again. If you still get a straight line for some species, try -t5.

kavazquez commented 2 years ago

Hi, did you solve this issue? I'm having the same problem with the straight line. Thanks!