I'm kind of new to this whole NGS and bioinformatics but I've found alot of answers from SEQanswers. Now I have question to which I didn't find an answer amongst the old posts and I'm stuck.
I'm trying to use mpileup to create a pileup file that has a set of SNP positions that I have selected before.
This is the comman that I'm usign:
samtools mpileup -f Gac_56_dna.fa -A -B 1rad_sort.bam -l 89cov50.bed > 1pileup
And I also tried:
samtools mpileup -f Gac_56_dna.fa -A -B -l 89cov50.bed 1rad_sort.bam > 1pileup
89cov50.bed is a bed format file with the SNP positions I would like to pull out from my bam file. Now it seems that my output pileup is not selected at all, but rather it seems that all of the unwanted SNP positions blead through to my output pileup. I also get the wanted SNP position in the output, but I wouldn't want to have those unwanted SNP positions in there.
Anyone have any idea what could be wrong here? Is it the order of my parameters in the command or is there something more to be added to -l than is said in the samtools manual? Any suggestions are wellcome at this point
Thanks!
I'm trying to use mpileup to create a pileup file that has a set of SNP positions that I have selected before.
This is the comman that I'm usign:
samtools mpileup -f Gac_56_dna.fa -A -B 1rad_sort.bam -l 89cov50.bed > 1pileup
And I also tried:
samtools mpileup -f Gac_56_dna.fa -A -B -l 89cov50.bed 1rad_sort.bam > 1pileup
89cov50.bed is a bed format file with the SNP positions I would like to pull out from my bam file. Now it seems that my output pileup is not selected at all, but rather it seems that all of the unwanted SNP positions blead through to my output pileup. I also get the wanted SNP position in the output, but I wouldn't want to have those unwanted SNP positions in there.
Anyone have any idea what could be wrong here? Is it the order of my parameters in the command or is there something more to be added to -l than is said in the samtools manual? Any suggestions are wellcome at this point
Thanks!