Hi all.
I am using mpileup to extract some sequencing information. However, when I tried to run mpileup with below command
samtools mpileup -C 50 -vu -t DP -t DV -t DPR -t DP4 -f human_g1k_v37.fasta -l ms_TAR22_mpileup.bed TAR22_N_Filtered_Sorted_Makrdup_Readgroup_Realigned_Recal.bam
The results are nothing except head file of VCF.
I think that the problems occur due to the -l option because when I removed -l options, it works well but the file size was very large to handle. When I chose -l option and run it, as I expected, then it failed to generate sequencing information related to -l files. I don't know why mpileup command doesn't output anything but its head even though I followed the manual and ran with the latest samtools version(1.2).
For your reference, here is the data inside my bed files.
22 24829532 24829532 ADORA2A
18 12449779 12449779 SPIRE1
12 123005948 123005948 RSRC2
12 25398281 25398281 KRAS
12 22354743 22354743 ST8SIA1
7 93055822 93055822 CALCR
2 170374777 170374777 KLHL41
1 158532510 158532510 OR6P1
1 79002163 79002163 PTGFR
Help me to get it!
1 answer
BED files are 0-based, half-open. What that means is that a SNV location needs to have a difference of 1 between the start and end location. In the case of your BED file, the locations appear to be in 1-based, closed coordinates. So, I suspect that mpileup is not using the BED file as you think. Try subtracting 1 from each element in column 2. Finally, make sure that the chromosome names match (including the "chr" or lack thereof).
•
written
by
Sean Davis
Log in to answer this question.