variant calling samtools

#1

Hello, I am having trouble when doing variant calling with samtools. I am getting only the header an no variants. If I would instead use Freebayes, I do get a lot of variables, and with Gatk, I get just a few. What can the problem be? Do I have to use different formats of bam input files, or different reference genome formats?

This is the command I am running:

samtools mpileup -go output/"$r1"/BWA_samtools_"$r1".bcf -f “$Re1” output/"$r1"/"$r1"RG_bwa.bam
bcftools call -vmO v -o output/"$r1"/BWA_samtools"$r1".vcf output/"$r1"/BWA_samtools_"$r1".bcf

and this is the empty header I am getting:

#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SRRsample_R1

thank you very much in advance!

#2

Are you developing a tool for galaxy? Your question looks like a more general bioinformatics question and not galaxy related. On a bio-it forum you would get a better and much faster answer.

Nevertheless, as far as my knowledge goes your command is not correct. You are missing a reference (-f) for mpileup. Also try to use bcftools mpileup because samtools mpileup is deprecated.

Have you seen this page already? Variant calling

#3

Thank you for your response! I am using a -f “$Re1” for a hg38 reference genome. I have seen that page, but it does not give me a hint on why is my command leading to no variants being found :frowning: