You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
Hi,
I am using OncoCNV 6.6 to get copy number estimates on exome data.
There is an error that comes up when running the ONCOCNV_getCounts.pl
$perl $TOOLDIR/ONCOCNV_getCounts.pl getControlStats -m Exon -b $targetBed -c $controls -o $OUTDIR/Control.stats.txt
reading NA12891_Capture.MarkDuplicates.mdup..GATK.Recalibrate.bam
sample name: NA12891_Capture.MarkDuplicates.mdup..GATK.Recalibrate
[ many lines counting reads ]
read 95700000 reads
Total target length: 0
processed 2 controls, NA12878_Capture.MarkDuplicates.mdup..GATK.Recalibrate NA12891_Capture.MarkDuplicates.mdup..GATK.Recalibrate
Can't use an undefined value as an ARRAY reference at
/opt/ONCOCNV-6.6/src//ONCOCNV_getCounts.pl line 450 (#1)
(F) A value used as either a hard reference or a symbolic reference must
be a defined value. This helps to delurk some insidious errors.
Uncaught exception from user code:
Can't use an undefined value as an ARRAY reference at /opt/ONCOCNV-6.6/src//ONCOCNV_getCounts.pl line 450.
the input files are :
bed file with the exome target regions
and a bam file processed with Picard MarkDuplicates, GATK Realign and Recalibrate.
Before any processing since the BAM file contains aligned reads to unplaced scaffolds which are not present in the target.bed I am filtering with samtools -L <target.bed>
Any advice/help/suggestions are welcome
Thanks
Konstantinos
The text was updated successfully, but these errors were encountered:
I meet this error too in 6.8 version
Total target length: 43760
processed 4 controls, D4_chr D5_chr D6_chr D8_chr
Can't use an undefined value as an ARRAY reference at
software/oncocnv/ONCOCNV-6.8/src//ONCOCNV_getCounts_b37.pl line 452 (#1)
(F) A value used as either a hard reference or a symbolic reference must
be a defined value. This helps to delurk some insidious errors.
Uncaught exception from user code:
Can't use an undefined value as an ARRAY reference at software/oncocnv/ONCOCNV-6.8/src//ONCOCNV_getCounts_b37.pl line 452
Hi,
I am using OncoCNV 6.6 to get copy number estimates on exome data.
There is an error that comes up when running the ONCOCNV_getCounts.pl
the input files are :
bed file with the exome target regions
and a bam file processed with Picard MarkDuplicates, GATK Realign and Recalibrate.
Before any processing since the BAM file contains aligned reads to unplaced scaffolds which are not present in the target.bed I am filtering with samtools -L <target.bed>
Any advice/help/suggestions are welcome
Thanks
Konstantinos
The text was updated successfully, but these errors were encountered: