SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
bcftools view generates an empty output manore Bioinformatics 14 07-08-2016 02:19 AM
How to view plink *.ld output rahulvrane Bioinformatics 0 10-12-2012 08:16 PM
View TopHat output xiaohua Bioinformatics 2 04-11-2012 05:11 PM
genotype in the output file of bcftools pengchy Bioinformatics 2 03-24-2012 10:52 AM
Can I view output the entire genome data? ardmore Bioinformatics 6 11-09-2011 01:21 PM

Reply
 
Thread Tools
Old 04-26-2013, 01:42 AM   #1
CowGirl
Junior Member
 
Location: Switzerland

Join Date: Mar 2013
Posts: 9
Default bcftools view output: afs

Hi everyone,
I've got a question about the output of bcftools view.

I'd like to call variants in 31 bam files with samtools.

Here's my command line:

HTML Code:
samtools mpileup -A -C50 -E -D -S -uf Chr24.fa *_chr24.bam | bcftools view -cvgb - > chr24.raw.bcf 2 > chr24.log
As output, I get the following:

HTML Code:
[bcfview] 100000 sites processed.
[afs] 0:96554.433 1:449.486 2:156.922 3:276.314 4:178.592 5:112.159 6:120.255 7:88.550 8:65.583 9:70.643 10:84.772 11:81.573 12:98.371 13:68.041 14:37.212 15:28.736 16:30.144 17:28.370 18:26.915 19:26.635 20:24.097 21:34.090 22:39.297 23:35.057 24:35.446 25:35.173 26:44.701 27:41.310 28:44.901 29:40.760 30:44.085 31:182.506 32:36.646 33:54.260 34:35.597 35:12.299 36:14.098 37:10.696 38:8.856 39:10.062 40:9.075 41:6.398 42:7.110 43:5.393 44:5.720 45:5.883 46:5.821 47:8.709 48:8.830 49:10.590 50:13.063 51:9.918 52:14.322 53:8.406 54:10.751 55:9.196 56:13.714 57:27.756 58:141.493 59:164.972 60:47.778 61:25.470 62:71.993
... and then I get different values for 200000, 300000 etc. sites processed.

What exactly do these numbers mean? I'd appreciate anyones help!

Cheers and thanks in advance
CowGirl is offline   Reply With Quote
Old 06-03-2013, 01:29 AM   #2
Lluc
Member
 
Location: Barcelona

Join Date: Aug 2010
Posts: 12
Default

As bcftools calls variants it reports the allele frequency spectrum (afs). You may be interested only in the last of these lines, when all sites have been processed. The lines starting with [afs] are a series of pairs n:m, where n goes from 0 to twice the number of (diploid) individuals in the sample (2N), and m is the expected number of variable sites where the alternative allele is present in exactly n copies out of 2N. These numbers are estimated from the genotype likelihoods and from a prior expectation of the distribution of alleles. The latter is controlled by the bcftools option -P. At the bottom of the following link you can see how to use the output of a previous run as a prior for the following in order to refine the estimate of the AFS.

http://samtools.sourceforge.net/samtools.shtml
Lluc is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 09:18 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO