Mutation callin For RNASeq

Question

[pinpoint]

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 .

[Amitm]

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.

[pinpoint]

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