Question: How can I input a BAM file to the samtools mpileup command without using a text file?
0
gravatar for cristian
3.0 years ago by
cristian240
cristian240 wrote:

Dear all,

I am using the following command:

samtools mpileup -t DP -u --fasta-ref output/genome/ref/seq/celegans.fa --bam-list BLAA.txt

to give a BAM file as an input to the 'samtools mpileup' command. The 'BLAA.txt' contains the location of my unique BAM file. Is there a way to give the name of the BAM file to the samtools mpileup command without creating this text file?

Thanks.

Cordially, C.

ADD COMMENTlink modified 3.0 years ago by genomax78k • written 3.0 years ago by cristian240
4

Hi, I hope that I understood right the question. I usually use this command:

samtools mpileup -f file.fa file.bam > output.pileup

therefore I give directly the bam file as input...

ADD REPLYlink written 3.0 years ago by noeD80
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