I try to run
bcftools to create a vcf file of my data, but I keep getting empty output files
The command I use are
bwa mem -t14 -M ~/genomes/Sce.R64-1-1/bwaIndex/Sce.R64-1-1 HHgDNA1.R1.fastq.gz HHgDNA1.R2.fastq.gz | samtools view -buh - | samtools sort -@ 14 -o bamFiles/bwa/HHgDNA1.sorted.bam samtools index bamFiles/bwa/HHgDNA1.sorted.bam bcftools mpileup -A -t 10 -Ou -f $REF_FASTA bamFiles/bwa/HHgDNA1.sorted.bam
$REF_FASTA is the fastA file also used to create the bwa indexed genome. I know the output goes to STDOUT, but I'm still trying to figure it out. looking at the bam files i have ~99% mapped and properly paired reads.
All I get is the header of the file, but nothing more.
any ideas what is going on?