abyzov
commented
4 years ago Hi, CNVnator is only intended to be used with WGS data. I can’t predict what kind of results it will produce for targeted sequencing.
Alexej Abyzov, Ph.D. Senior Associate Consultant, Assistant Professor of Biomedical Informatics, Department of Health Sciences Research, Center for Individualized Medicine, Mayo Clinic
Mayo Clinic, 200 1st street SW, Harwick 3-12 Rochester, MN 55905 www.abyzovlab.orghttp://www.abyzovlab.org tel: +1-(507)-538-0978 fax: +1-(507)-284-0745
Hello, I'm using CNVnator to call CNV for a specific region of genome (targeted sequencing data) located on chromosome 8. I don't see any error in running the CNVnator, but the CNV results do not make sense. Here is the output: [abdollahiarp@i21a-s2 CNVnator]$ cat SAMPLE.chr8.tsv deletion 8:1-67213000 6.7213e+07 9.51699e-05 2.37116e-15 0 2.37123e-15 0 -1 duplication 8:67213001-77212000 9.999e+06 14.3563 0 0 0 0 1 deletion 8:77212001-113320000 3.6108e+07 1.11573e-05 4.41377e-15 0 4.41402e-15 0 1
the header of chr8.fa file:
The header of *.bam file: samtools view -h ../chr8_target.bam|head @HD VN:1.5 GO:none SO:coordinate @SQ SN:1 LN:158534110 @SQ SN:2 LN:136231102 @SQ SN:3 LN:121005158 @SQ SN:4 LN:120000601 @SQ SN:5 LN:120089316 @SQ SN:6 LN:117806340 @SQ SN:7 LN:110682743 @SQ SN:8 LN:113319770
I think something is wrong with my *.bam file. The targeted region was extracted by samtools using the following command: samtools view input.bam 8:67212333-77212333 -b > chr8_target.bam
the depth of sequencing for target region is ~40X and coverage is %99.
Looking forward to your help. Thanks very much in advance,
Rostam,