Generate VCF from different .bam files with different chromosome names I have two resources of .bam files. One is generated by our lab (1 sample = 1 bam). One is downloaded online (again 1 sample = 1 bam). For the downloaded samples the chromosomes are labelled: chr1, chr2, chr3 etc For our lab samples, the chromosomes are labelled: 1, 2, 3 etc. I want to generate a single VCF file of variants across all samples.

I'm using bcftools:

bcftools mpileup -Ov -f ref.fasta -b samples.txt | bcftools call -mv -o bamMge.vcf


However, I get no calls and the repeated error: [E::faidx_adjust_position] The sequence "1" was not found

I have two questions:


Is my strategy correct (i.e. bcftools mpileup)? Do I need to incorporate extra steps (NB I also have matching gVCF files)
How can I either (i) alter the chromosome labeling of one of the subsets of bam files, or, (ii) use a mapping file to match chromosome labels during the mpileup run?


Thanks
The main issue here is that your bam files have different chromosome labels. (i.e. 1,2,3 vs. chr1,chr2,chr3) as you mentioned.

This suggests that the data was mapped to a slightly different version of the reference genome. As a first layer, you might want to double check that these reference chromosomes are cross compatible (e.g. both correspond to hg19 for instance). To find more information on the reference genome used, you can check the header information using "samtools view -H "

Assuming that the reference genomes are cross compatible, you can try converting it to sam, adding the missing "chr" label in a pipe, and converting it back to a bam file. However, this will also require modification of the header file which can be challenging in itself.

The easiest (and more rigorous) approach is probably just to convert the batch of bam files with the wrong chromosome labels back into fastq files. You will then want to remap them using the exact same reference genome as the other batch of bam files. After which, you should be able to perform variant calling on the combined batch of bam files.