Hello everyone,
I am generating coverage tables (tables containing the coverage for each base in the reference genome), and I found 2 ways to do this:
1) BAM -> BCF -> VCF
2) BAM -> pileup
As it turns out, pileup and VCF format have some discrepencies in coverages of bases, which means that when filtering entries for a coverage of 15, pileup returns more bases. However, I do not understand why this happens. The alignment files are generated with BWA and converted to BAM using SAMtools, including sorting, removing duplicates and and indexing.
So does anyone know the difference between the 2 methods which causes the coverage differences?
I am generating coverage tables (tables containing the coverage for each base in the reference genome), and I found 2 ways to do this:
1) BAM -> BCF -> VCF
Code:
./samtools mpileup -u $SAMPLE_ID.rmdup-S.bam > $SAMPLE_ID.bcf ./bcftools/bcftools view $SAMPLE_ID.bcf > $SAMPLE_ID.vcf
Code:
./samtools pileup -f $REFERENCE $SAMPLE_ID.rmdup-S.bam > $SAMPLE_ID.pileup
So does anyone know the difference between the 2 methods which causes the coverage differences?
