Does the input BAM file need to remove PCR duplicate reads? about cnvcaller HOT 4 CLOSED

Yes, you should mask the PCR duplication before calling.

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Thank you, teacher!
But when I use "Individual.Process.sh" shell file , I encountered a new problem.
my command is:
bash ~/CNVcaller/Individual.Process.sh -b THH001.RD.bam -h THH001 -d Sscrofa11.1_800_link -s X > $path/CNVcaller/log/THH001_absolute.log 2>&1
and the log file:
CNVcaller install directory /public/home/qiuyb/CNVcaller
refdb /public/home/qiuyb/CNV/CNVcaller/referenceDB.800
header THH001
duplicate file Sscrofa11.1_800_link
bam /public/home/qiuyb/CNV/RD_method/THH001.RD.bam
sex X
windowsize 800
stats read depth per window start!
Mon Nov 2 20:01:19 2020
Parsing sample THH001 ...
/public/home/qiuyb/CNV/RD_method/THH001.RD.bam file loading done!Mon Nov 2 20:22:58 2020
completed bam parsing!
raw reads count finished!
raw reads count file loading finished!
Use of uninitialized value $pos in hash element at /public/home/qiuyb/CNVcaller/bin/1.2.CNVcorrect.pl line 23, line 1.
Use of uninitialized value $pos in hash element at /public/home/qiuyb/CNVcaller/bin/1.2.CNVcorrect.pl line 23, line 2.
Use of uninitialized value $pos in hash element at /public/home/qiuyb/CNVcaller/bin/1.2.CNVcorrect.pl line 23, line 3.
.........
.........
.........
duplicated window record file loading finished!
corrected window number: 0
absolute reads counts correction finished!
absolute correct finished!
.........
.........
.........

Is this caused by the link file? Do I need to generate a link file by myself?

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Hello, teacher. I’ve solved this problem by creating my own link file. The pig link file downloaded from the AOD site appears to be different from the demo link (name: dupfile) you provided.
the Sscrofa11.1_800_link downloaded from AOD website:
CM000812.5-100026801 CM000812.5-100026401 KQ004242.1_2642000_2644000-1601 KQ004242.1_2642000_2644000-1201 CM000812.5-100026801
CM000812.5-100062001 LUXW01012492.1_644000_645615-401 CM000812.5-100061601 LUXW01012492.1_644000_645615-1 CM000812.5-100062001
CM000812.5-100062401 LUXW01012492.1_644000_645615-801 LUXW01012492.1_644000_645615-401 CM000812.5-100062401 CM000812.5-100062001
.....
and demo link file:
29:10068501 29:10068501 29:37307501 29:30795001
29:10069001 29:10069001 29:6289001 29:3501501 29:22485501 29:9795001 29:39989001 29:5863001 29:37307001
......
......
But when I created the mergeCNVR file using the CNV.Discovery.sh , a new error occurred......
the log file:
nohup: ignoring input
CNVcaller install directory /public/home/qiuyb/CNVcaller
referenceDB /public/home/qiuyb/CNV/CNVcaller/referenceDB.800
normalizedFileList list
excludedFileList exclude_list
windowsize 800
frequency 0.1
homozygous 3
pearsonCorrelation 0.5
primaryCNVR primaryCNVR
mergedCNVR mergeCNVR
2.16078947368421
/public/home/qiuyb/CNV/CNVcaller/RD_normalized/DHB00011_mean_70.38_SD_11.40_sex_1 0.35
/public/home/qiuyb/CNV/CNVcaller/RD_normalized/DHB00020_mean_97.02_SD_13.72_sex_1 0.35
/public/home/qiuyb/CNV/CNVcaller/RD_normalized/DHB0004_mean_102.06_SD_14.12_sex_1 0.35
sample number: 3
effective sample: 3
pearson correlation: 0.5
define effective window finished!
refine effective window finished!
primary CNVR define finished!
length() used on @tmp_start_array (did you mean "scalar(@tmp_start_array)"?) at /public/home/qiuyb/CNVcaller/bin/2.2.CNVRRedundancy.pl line 48.
length() used on @tmp (did you mean "scalar(@tmp)"?) at /public/home/qiuyb/CNVcaller/bin/2.2.CNVRRedundancy.pl line 48.
merge CNVR finished!

It seems somthing wrong in 2.2.CNVRRedundancy.pl .......I was so confused. Could this be an error caused by the Perl version？

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I tried changing the Perl version to 5.10.1 using perlbrew. And then it’s back to normal !!!
Thank you teacher.

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