Mutation callin For RNASeq
0
0
Entering edit mode
3 months ago
pinpoint • 0

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 .

STAR • 288 views
1
Entering edit mode

Hi, It just might be due to difference in default BAM compression levels used by the different programs. Use could use samtools flagstat on your prev. and post-'RG' tag added BAMs to confirm that the number of reads in either file are the same.

0
Entering edit mode

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