Open DarioS opened 2 years ago
Some of the required elements are missing due to bugs in gatk4_pon_check_sample.sh. Example output:
gatk4_pon_check_sample.sh
../Reference/hs38DH.fasta,CSCC_0153-B1,,0142-scattered.interval_list,,,./Logs/gatk4_pon ../Reference/hs38DH.fasta,CSCC_0163-B1,,2903-scattered.interval_list,,,./Logs/gatk4_pon
We see that the third element is blank. $bam is undefined. Similarly, fifth and sixth elements are missing. $out and $nt are undefined.
$bam
$out
$nt
In summary
echo "${ref},${sample},${bam},${intfile},${out},${nt},${logdir}" >> ${inputfile}
makes use of multiple undefined variables, causing errors when the intervals are re-run.
Some of the required elements are missing due to bugs in
gatk4_pon_check_sample.sh. Example output:We see that the third element is blank.
$bamis undefined. Similarly, fifth and sixth elements are missing.$outand$ntare undefined.In summary
makes use of multiple undefined variables, causing errors when the intervals are re-run.