I have file.bam around 4.6 GB and converted it to file.pileup around 8.3 GB by samtools:
samtools mpileup -B -f genome.fa file.bam > file.pileup
then I used VarScan to call variants like:
java -Xmx2g -jar $VARSCAN_DIR/VarScan.v2.3.7.jar mpileup2snp file.pileup --min-coverage 10 --min-base-qual 30 --output-vcf 1 > sample1.vcf
But the sample.vcf is too small which is 11,450 KB
So anyone know how I can make sure that the bam file is acceptable to get pileup file?
and also how I can know that pileup file is good input in VarScan?
Thank you in advance for your help