COSMIC vcf file contains "N" & "." characters in ALT column

vipul jain · 09-02-2015, 11:40 PM

Hi,

I am using COSMIC hg19 vcf file to make hotspot bed file but in ALT column of COSMIC vcf contains "N" & "." characters so software i am using ignores that COSMIC ID while making hotspot bed file. It will be great if anybody could help me.

lindenb · 09-03-2015, 01:16 AM

cross posted: https://www.biostars.org/p/103846/#156651

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
glimmer .predict file: "from" larger than "to" on + strand	shany	Bioinformatics	0	05-27-2014 03:21 PM
Dealing with ">" and "<" signs in mapping column in RNA-Seq pileup file for RNA-edit	slp	Bioinformatics	0	03-21-2014 10:18 AM
"allele balance ratio" and "quality by depth" in VCF files	efoss	Bioinformatics	2	10-25-2011 12:13 PM
The position file formats ".clocs" and "_pos.txt"? Ist there any difference?	elgor	Illumina/Solexa	0	06-27-2011 08:55 AM
"Systems biology and administration" & "Genome generation: no engineering allowed"	seb567	Bioinformatics	0	05-25-2010 01:19 PM

09-02-2015, 11:40 PM	#1
vipul jain Junior Member Location: Nashik Join Date: Apr 2014 Posts: 7	COSMIC vcf file contains "N" & "." characters in ALT column Hi, I am using COSMIC hg19 vcf file to make hotspot bed file but in ALT column of COSMIC vcf contains "N" & "." characters so software i am using ignores that COSMIC ID while making hotspot bed file. It will be great if anybody could help me.

09-03-2015, 01:16 AM	#2
lindenb Senior Member Location: France Join Date: Apr 2010 Posts: 143	cross posted: https://www.biostars.org/p/103846/#156651