Mutation callin For RNASeq
i want to run mutect2 for RNASeq bam of Star output , but while adding @RG header via samtool or picard ,the file size reduces 1 to 2 GB.of the new bam, why so. Does it effect the quality of vcf file .
• 1,046 views
•
link
written
by
pinpoint •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
How to keep only first part of the name when adding AddOrReplaceReadGroups in multiple BAM files …
written by kabir.deb •
-
Bam file from STAR
written by Chris •
-
Filter variants supported by 20% of total reads
written by Ks-seq •
-
GATK GetSampleName is not working?
written by imanthony1993 •
-
BAM File size increased after extracting unique reads
written by ilovesuperheroes1993 •
-
How treat a Bam file with mutiple read groups (RG)
written by zamani_2012 •
-
Sorted vs unsorted SAM/BAM
written by ofonov •
-
Managing large data sets
written by umn_bist •
-
Add read group to header after samtools merge
written by dariober
-
Picard Addreplacereadgroup Error: Rg Id Not Found In Header
written by William
Hi, It just might be due to difference in default BAM compression levels used by the different programs. Use could use
samtools flagstaton your prev. and post-'RG' tag added BAMs to confirm that the number of reads in either file are the same.thanks for considering my query .. Files are same but size differs , further more when I run mutect2 call for variants it gives a vcf file with empty reads. how is it so ? I used mutect2