I am also trying to check the coverage at each position of my reference using the CoverageBySample tool (with and without the –L argument):
java -Xmx30g -jar GenomeAnalysisTK.jar \ -T UnifiedGenotyper \ –T CoverageBySample \ –R ref.fasta \ -I input.bam \ -o output.cov\
The output (below) is giving the right coverage but without the positions on the reference and also skipping all positions with no coverage. Is there any way to get these positions in the output file?
eo78 10 eo78 10 eo78 10 eo78 10 eo78 10 eo78 11 eo78 12 eo78 12 eo78 12