Pindel Error: I cannot find the file in configuration file

Question

[arya.sagittarius]

Hi,

I come across this error while running pindel v0.3 in docker. My bam file is named main.clean.bam and my config file has:

main.clean.bam 270 main

The error is:

I cannot find the file 'main.clean.bam'. referred to in configuration file 'calls/pindel_config.txt'. Please change the BAM configuration file.

Any idea how to sort this issue.

Thanks in advance

Answer 1

[ATpoint]

Give it the full path to the file, get it with realpath main.clean.bam and provide that in the config file.

[arya.sagittarius]

Thank you. this worked :)