Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
I have another problem: when using vcf0=, followed by files locations separated by comma, callvariants.sh create subdirectory instead of just creating files at specified location.
-
Same error here: downloaded BBMap 2 weeks ago, finishing my snp calling pipeline today, same problem and discovering the patch went out 10 days ago...
Thx for the fix
Leave a comment:
-
Hi Greg,
Sorry about that, there was a bug that slipped in around v37.87 with regards to multisample VCF names. It's fixed in v37.96 which I will release this week.
-Brian
Leave a comment:
-
bbmap callvariants.sh multisample vcf format, wrong number of fields
Trying to use BBMap callvariants on multiple samples. The resulting VCF does not have the sample names and yields an error with any vcf tools:
Code:vcf-validator tmp.vcf Wrong number of fieldsin tmp.vcf; expected 15, got 16. The offending line was: [... the first line of variants]
Code:#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT FORMAT FORMAT FORMAT FORMAT FORMAT FORMAT
Code:callvariants.sh multisample=t list=SamList out=tmp.vcf ref=genome.fa #ive also tried using the output command, no change callvariants.sh multisample=t list=SamList out=tmp.vcf ref=genome.fa vcf0=S1,S2,S3,S4,S5,S5 #As well as each sample using the "in" command callvariants.sh multisample=t in=S1.sam,S2.sam,S3.sam,S4.sam,S5.sam,S6.sam out=tmp.vcf ref=genome.fa overwrite=t vcf0=AO,GG,OG,SF,TH,Tum
Latest Articles
Collapse
-
by seqadmin
The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...-
Channel: Articles
04-22-2024, 07:01 AM -
-
by seqadmin
Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...-
Channel: Articles
04-04-2024, 04:25 PM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, Yesterday, 11:49 AM
|
0 responses
13 views
0 likes
|
Last Post
by seqadmin
Yesterday, 11:49 AM
|
||
Started by seqadmin, 04-24-2024, 08:47 AM
|
0 responses
16 views
0 likes
|
Last Post
by seqadmin
04-24-2024, 08:47 AM
|
||
Started by seqadmin, 04-11-2024, 12:08 PM
|
0 responses
61 views
0 likes
|
Last Post
by seqadmin
04-11-2024, 12:08 PM
|
||
Started by seqadmin, 04-10-2024, 10:19 PM
|
0 responses
60 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 10:19 PM
|
Leave a comment: