PSMC with option -d
Hi!
I want to get the local TMRCA for each locus from PSMC, so I use -d option.
Could anyone tell me, which column is the local TMRCA from output file DC line?
Thank you so much!
psmc
software error
• 1,620 views
•
link
written
by
jinzheng9406 •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
PSMC -p parameter
written by Alba •Hello, I am trying to implement PSMC in some analyses I with dummy data to fully understand how does this software work. However, I am …
-
Extract out lines with 's__' into a new file together with first two lines of the file
written by dpcHi community!!! I have a [metaphlan output file][1] from where I want to extract the first two lines (starting with "ID" and "#SampleID") along with …
-
Why my PSMC analysis can't trace further back to 1Mya?
written by llq0325 •Hi! I'm using PSMC to estimate historical effective population size. However, the earliest time PSMC can trace back to is ~0.1 Mya (g=5, m=2.5e-8). Could …
-
How to get a fake diploid sequence(each one from a population)
written by jinzheng9406 •I want to use PSMC to analysis the division time of two closely human population. For that, I need to construct a pseudo-diploid sequence. Now, …
-
An error when I used vcfutils vcf2fq
written by jinzheng9406 •I try to use vcfutils convert a vcf file which have been process by bcftools view. But when I run the commond 'vcfutils vcf2fq xxx.vcf …
-
How to use samtools/bcftoos/vcfutils to call SNP
written by jinzheng9406 •I want to analysis a genome with PSMC After that, I want to use samtools/bcftools/vcfutils to process the data. And I want to follow these …
-
How to locate a locus on the genome and get the Exon/Intron No.
written by shiyang93 •HI, I have a set of locus: chr2:123456-234567......,now I want to know if this locus is on a gene, if it is, then on which …
-
How to get HGVS notation of protein form genome snp vcf
written by yixinrufeng •Hi everyone I want to do variation annotation with PROVEAN (http://provean.jcvi.org/seq_submit.php) on non-module organisms, I have got protein sequence of my study species from MAKER, …
-
How to interpret the outputs generated from bamtobed using BedTools?
written by Louis Kok •Hi All, I have generated a bed file from a BAM file using bamtobed commands from BedTools. I am not sure how to interpret the …
-
Extracting Info From A Column Of Vcf File?
written by bioinfo<p>I used the command below to get column 2,6 and 8 of my vcf file</p> <pre><code>cut -f 2,6,8 my.vcf > out.vcf </code></pre> <p>output:</p> <pre><code>12 AA …
Please, expand the abbreviations.
TMRCA = Time of most recent common ancestor. PSMC = pairwise sequentially Markovian coalescent, a software developed by Heng Li
DC is a line name in the PSMC output file.