How can I input a BAM file to the samtools mpileup command without using a text file?
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.
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biomagician
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Hi, I hope that I understood right the question. I usually use this command:
therefore I give directly the bam file as input...