I am trying to call SNPs with at least 1X depth (My estimation is that most of the SNPs I want to see have indeed 1X / 2X depth). I have mapped consensus sequences to the Tomato reference genome (generating in theory 1X/2X depth on specific target positions) with Bowtie2 and perform SNP/INDEL calling with samtools mpileup and bcftools. However, I can't retrieve SNPs with 1X depth although I do mention it on the command line. Can anyone help me?
for directory in *; do for file in $directory/*sorted*; do prefix=$(echo $file | rev | cut -f1 -d '/' | rev | cut -f1 -d '.'); samtools mpileup -uf ../../Data/SolanumLycopersicum_gDNA_2.40.fa $file | bcftools view -bvcg - > $directory/$prefix.bcf & done; done for directory in *; do for file in $directory/*bcf*; do prefix=$(echo $file | rev | cut -f1 -d '/' | rev | cut -f1 -d '.'); bcftools view $file | vcfutils.pl varFilter -d1 -D100 > $directory/$prefix.vcf & done; done