lh3
Erroneous Result（Straight line）
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.
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!
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!
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.
Hi, did you solve this issue? I'm having the same problem with the straight line. Thanks!
