How can I input a BAM file to the samtools mpileup command without using a text file?
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4.6 years ago
cristian ▴ 290

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.

samtools mpileup bam variant calling • 3.1k views
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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...

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