Error: RSEM Bam file for variant calling

Question

[kartikayprasad]

Hi Everyone, I hope everyone is doing fine in this pandemic period.

I have prepared the reerence of human genome(Grch38) using the following command:

rsem-prepare-reference -gtf Gen.gtf --bowtie2 Genome.fa Genome

and then calculate the count data using the

  > rsem-calculate-expression command

I noticed that in the output mapping bam file, instead of chromosome name, the Rsem is using the transcript id.

I further try to call the variants using the bcftools, for which i again have to provide the reference genome along with mapped bam file in command

bcftools mpileup -f Genome.fa alignments.bam | bcftools call -mv -Ov -o variant.vcf

Error: While running the above command the bctool is giving the error because it is not able to match the chromosome names from genome.fa file to mapped.bam file becasue the Rsem used the transcript id instead of chromosome name while make index o genome and mapping of reads.

Can anyone help me regarding the situation. I need to call the variants.

[GenoMax]

It is better to use 101010 button to format code portion of your post.