Problem generating a .vcf after upgrade of samtools and bcftools

Question

[Andy]

Hi I used to go over candidate sites of variation using SAMtools mpileup after which I used to execute some evaluations of the data using BCFtools. In general I used to provide the reference fasta genome and use the options -u and -v to generate the output in VCF format for post analysis.

Therefore, I used to execute something like this:

samtools mpileup -v -u -f  /temp/data-u_0.v7.fas /temp/data-alignBAM-sorted.bam  > /temp/wgs-data-alignBAM-sorted.mpileup.vcf

I updated my tools recently because I changed my computer, and when I executed the previously discussed, I received a reject of samtools of my execution(), I checked the samtool's man, and says that vcf from samtools is no longer generated, and theorically must be generated from bcftools, but, I can't find the way using the man documentation of bcftools to get a .vcf from a sorted .bam file.

• bcftools-1.17
• samtools-1.17

I would appreciate any help with this, thank you

Answer 1

[GenoMax]

I can't find the way using the man documentation of bcftools to get a .vcf from a sorted .bam file.

This should be all you need: https://samtools.github.io/bcftools/howtos/variant-calling.html

[Andy]

Really the only needed, that help worked, thank's

Answer 2

[jkbonfield]

Use bcftools mpileup instead of samtools mpileup and it'll probably work fine. There may be a few minor differences, but by and large the syntax is identical.