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!