CoNIFER (copy number inference from exome reads) uses exome sequencing data to find copy number variants (CNVs) and genotype the copy-number of duplicated genes. It can reliably be
used to discover disruptive genic CNVs missed by standard approaches and should have broad
application in human genetic studies of disease.
Allocate an interactive session and run the program. Sample session:
[user@biowulf]$ sinteractive [user@cn3144 ~]$ module load conider [+] Loading singularity 3.10.5 on cn4198 [+] Loading conifer 0.2.2
[user@cn3144 ~]$ python-c conifer.py -h
usage: CoNIFER [-h] [--version] {rpkm,analyze,export,plot,call,plotcalls} ...
This is CoNIFER 0.2.2 (Copy Number Inference From Exome Reads), designed to
detect and genotype CNVs and CNPs from exome sequence read-depth data. See
Krumm et al., Genome Research (2012) doi:10.1101/gr.138115.112 Niklas Krumm,
2012 nkrumm@uw.edu
positional arguments:
{rpkm,analyze,export,plot,call,plotcalls}
Command to be run.
rpkm Create an RPKM file from a BAM file
analyze Basic CoNIFER analysis. Reads a directory of RPKM
files and a probe list and outputs a HDF5 file
containing SVD-ZRPKM values.
export Export SVD-ZRPKM values from a HDF5 file to bed or vcf
format.
plot Plot SVD-ZRPKM values using matplotlib
call Very rudimentary caller for CNVs using SVD-ZRPKM
thresholding.
plotcalls Make basic plots from call file from "call" command.
optional arguments:
-h, --help show this help message and exit
--version show program's version number and exit
[user@cn3144 ~]$ cp $CONIFER_DATA/* .
[user@cn3144 ~]$ conifer.py analyze --probes probes.txt --rpkm_dir RPKM_data/ --output analysis.hdf5 --svd 6 --write_svals singular_values.txt
[INIT] Successfully read in 194080 probes from probes.txt
[INIT] Found 26 RPKM files in RPKM_data/
[INIT] Mapping file to sampleID: RPKM_data/NA12878.txt --> NA12878
[INIT] Mapping file to sampleID: RPKM_data/NA15510.txt --> NA15510
[INIT] Mapping file to sampleID: RPKM_data/NA18507.txt --> NA18507
[INIT] Mapping file to sampleID: RPKM_data/NA18517.txt --> NA18517
[INIT] Mapping file to sampleID: RPKM_data/NA18555.txt --> NA18555
[INIT] Mapping file to sampleID: RPKM_data/NA18956.txt --> NA18956
[INIT] Mapping file to sampleID: RPKM_data/NA19129.txt --> NA19129
[INIT] Mapping file to sampleID: RPKM_data/NA19240.txt --> NA19240
[INIT] Mapping file to sampleID: RPKM_data/Trio1.fa.txt --> Trio1.fa
[INIT] Mapping file to sampleID: RPKM_data/Trio1.mo.txt --> Trio1.mo
[INIT] Mapping file to sampleID: RPKM_data/Trio1.p1.txt --> Trio1.p1
[INIT] Mapping file to sampleID: RPKM_data/Trio2.fa.txt --> Trio2.fa
[INIT] Mapping file to sampleID: RPKM_data/Trio2.mo.txt --> Trio2.mo
[INIT] Mapping file to sampleID: RPKM_data/Trio2.p1.txt --> Trio2.p1
[INIT] Mapping file to sampleID: RPKM_data/Trio3.fa.txt --> Trio3.fa
[INIT] Mapping file to sampleID: RPKM_data/Trio3.mo.txt --> Trio3.mo
[INIT] Mapping file to sampleID: RPKM_data/Trio3.p1.txt --> Trio3.p1
[INIT] Mapping file to sampleID: RPKM_data/Trio4.fa.txt --> Trio4.fa
[INIT] Mapping file to sampleID: RPKM_data/Trio4.mo.txt --> Trio4.mo
[INIT] Mapping file to sampleID: RPKM_data/Trio4.p1.txt --> Trio4.p1
[INIT] Mapping file to sampleID: RPKM_data/Trio5.fa.txt --> Trio5.fa
[INIT] Mapping file to sampleID: RPKM_data/Trio5.mo.txt --> Trio5.mo
[INIT] Mapping file to sampleID: RPKM_data/Trio5.p1.txt --> Trio5.p1
[INIT] Mapping file to sampleID: RPKM_data/Trio6.fa.txt --> Trio6.fa
[INIT] Mapping file to sampleID: RPKM_data/Trio6.mo.txt --> Trio6.mo
[INIT] Mapping file to sampleID: RPKM_data/Trio6.p1.txt --> Trio6.p1
[INIT] Successfully read RPKM data for sampleID: Trio6.mo
[INIT] Successfully read RPKM data for sampleID: Trio4.mo
[INIT] Successfully read RPKM data for sampleID: Trio3.fa
[INIT] Successfully read RPKM data for sampleID: Trio1.fa
[INIT] Successfully read RPKM data for sampleID: Trio2.mo
[INIT] Successfully read RPKM data for sampleID: Trio3.p1
[INIT] Successfully read RPKM data for sampleID: Trio4.fa
[INIT] Successfully read RPKM data for sampleID: Trio5.fa
[INIT] Successfully read RPKM data for sampleID: Trio2.fa
[INIT] Successfully read RPKM data for sampleID: Trio1.mo
[INIT] Successfully read RPKM data for sampleID: NA18517
[INIT] Successfully read RPKM data for sampleID: NA12878
[INIT] Successfully read RPKM data for sampleID: Trio5.p1
[INIT] Successfully read RPKM data for sampleID: NA18507
[INIT] Successfully read RPKM data for sampleID: NA18555
[INIT] Successfully read RPKM data for sampleID: NA15510
[INIT] Successfully read RPKM data for sampleID: NA18956
[INIT] Successfully read RPKM data for sampleID: Trio2.p1
[INIT] Successfully read RPKM data for sampleID: Trio3.mo
[INIT] Successfully read RPKM data for sampleID: NA19240
[INIT] Successfully read RPKM data for sampleID: Trio6.fa
[INIT] Successfully read RPKM data for sampleID: Trio5.mo
[INIT] Successfully read RPKM data for sampleID: Trio4.p1
[INIT] Successfully read RPKM data for sampleID: Trio1.p1
[INIT] Successfully read RPKM data for sampleID: NA19129
[INIT] Successfully read RPKM data for sampleID: Trio6.p1
[INIT] Finished reading RPKM files. Total number of samples in experiment: 26 (0 failed to read properly)
[INIT] Attempting to process chromosomes: chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY
[RUNNING: chr1] Now on: chr1
[RUNNING: chr1] Found 19822 probes; probeID range is [0-19822]
[RUNNING: chr1] Calculating median RPKM
[RUNNING: chr1] Masking 412 probes with median RPKM < 1.000000
[RUNNING: chr1] Calculating ZRPKM scores...
[RUNNING: chr1] SVD decomposition...
[RUNNING: chr1] Saving SVD-ZRPKM values
...
[RUNNING: chr2] Now on: chr2
[RUNNING: chr2] Found 14782 probes; probeID range is [19822-34604]
[RUNNING: chr2] Calculating median RPKM
[RUNNING: chr2] Masking 280 probes with median RPKM < 1.000000
[RUNNING: chr2] Calculating ZRPKM scores...
[RUNNING: chr2] SVD decomposition...
[RUNNING: chr2] Saving SVD-ZRPKM values
[RUNNING: chr3] Now on: chr3
[RUNNING: chr3] Found 11714 probes; probeID range is [34604-46318]
[RUNNING: chr3] Calculating median RPKM
[RUNNING: chr3] Masking 207 probes with median RPKM < 1.000000
[RUNNING: chr3] Calculating ZRPKM scores...
[RUNNING: chr3] SVD decomposition...
[RUNNING: chr3] Saving SVD-ZRPKM values
[RUNNING: chr4] Now on: chr4
[RUNNING: chr4] Found 7549 probes; probeID range is [46318-53867]
[RUNNING: chr4] Calculating median RPKM
[RUNNING: chr4] Masking 142 probes with median RPKM < 1.000000
[RUNNING: chr4] Calculating ZRPKM scores...
[RUNNING: chr4] SVD decomposition...
[RUNNING: chr4] Saving SVD-ZRPKM values
[RUNNING: chr5] Now on: chr5
[RUNNING: chr5] Found 8602 probes; probeID range is [53867-62469]
[RUNNING: chr5] Calculating median RPKM
[RUNNING: chr5] Masking 168 probes with median RPKM < 1.000000
[RUNNING: chr5] Calculating ZRPKM scores...
[RUNNING: chr5] SVD decomposition...
[RUNNING: chr5] Saving SVD-ZRPKM values
[RUNNING: chr6] Now on: chr6
[RUNNING: chr6] Found 9221 probes; probeID range is [62469-71690]
[RUNNING: chr6] Calculating median RPKM
[RUNNING: chr6] Masking 284 probes with median RPKM < 1.000000
[RUNNING: chr6] Calculating ZRPKM scores...
[RUNNING: chr6] SVD decomposition...
[RUNNING: chr6] Saving SVD-ZRPKM values
[RUNNING: chr7] Now on: chr7
[RUNNING: chr7] Found 9213 probes; probeID range is [71690-80903]
[RUNNING: chr7] Calculating median RPKM
[RUNNING: chr7] Masking 217 probes with median RPKM < 1.000000
[RUNNING: chr7] Calculating ZRPKM scores...
[RUNNING: chr7] SVD decomposition...
[RUNNING: chr7] Saving SVD-ZRPKM values
[RUNNING: chr8] Now on: chr8
[RUNNING: chr8] Found 6597 probes; probeID range is [80903-87500]
[RUNNING: chr8] Calculating median RPKM
[RUNNING: chr8] Masking 137 probes with median RPKM < 1.000000
[RUNNING: chr8] Calculating ZRPKM scores...
[RUNNING: chr8] SVD decomposition...
[RUNNING: chr8] Saving SVD-ZRPKM values
[RUNNING: chr9] Now on: chr9
[RUNNING: chr9] Found 7887 probes; probeID range is [87500-95387]
[RUNNING: chr9] Calculating median RPKM
[RUNNING: chr9] Masking 216 probes with median RPKM < 1.000000
[RUNNING: chr9] Calculating ZRPKM scores...
[RUNNING: chr9] SVD decomposition...
[RUNNING: chr9] Saving SVD-ZRPKM values
[RUNNING: chr10] Now on: chr10
[RUNNING: chr10] Found 8018 probes; probeID range is [95387-103405]
[RUNNING: chr10] Calculating median RPKM
[RUNNING: chr10] Masking 141 probes with median RPKM < 1.000000
[RUNNING: chr10] Calculating ZRPKM scores...
[RUNNING: chr10] SVD decomposition...
[RUNNING: chr10] Saving SVD-ZRPKM values
[RUNNING: chr11] Now on: chr11
[RUNNING: chr11] Found 10857 probes; probeID range is [103405-114262]
[RUNNING: chr11] Calculating median RPKM
[RUNNING: chr11] Masking 194 probes with median RPKM < 1.000000
[RUNNING: chr11] Calculating ZRPKM scores...
[RUNNING: chr11] SVD decomposition...
[RUNNING: chr11] Saving SVD-ZRPKM values
[RUNNING: chr12] Now on: chr12
[RUNNING: chr12] Found 10976 probes; probeID range is [114262-125238]
[RUNNING: chr12] Calculating median RPKM
[RUNNING: chr12] Masking 172 probes with median RPKM < 1.000000
[RUNNING: chr12] Calculating ZRPKM scores...
[RUNNING: chr12] SVD decomposition...
[RUNNING: chr12] Saving SVD-ZRPKM values
[RUNNING: chr13] Now on: chr13
[RUNNING: chr13] Found 3475 probes; probeID range is [125238-128713]
[RUNNING: chr13] Calculating median RPKM
[RUNNING: chr13] Masking 81 probes with median RPKM < 1.000000
[RUNNING: chr13] Calculating ZRPKM scores...
[RUNNING: chr13] SVD decomposition...
[RUNNING: chr13] Saving SVD-ZRPKM values
[RUNNING: chr14] Now on: chr14
[RUNNING: chr14] Found 6098 probes; probeID range is [128713-134811]
[RUNNING: chr14] Calculating median RPKM
[RUNNING: chr14] Masking 113 probes with median RPKM < 1.000000
[RUNNING: chr14] Calculating ZRPKM scores...
[RUNNING: chr14] SVD decomposition...
[RUNNING: chr14] Saving SVD-ZRPKM values
[RUNNING: chr15] Now on: chr15
[RUNNING: chr15] Found 6766 probes; probeID range is [134811-141577]
[RUNNING: chr15] Calculating median RPKM
[RUNNING: chr15] Masking 124 probes with median RPKM < 1.000000
[RUNNING: chr15] Calculating ZRPKM scores...
[RUNNING: chr15] SVD decomposition...
[RUNNING: chr15] Saving SVD-ZRPKM values
[RUNNING: chr16] Now on: chr16
[RUNNING: chr16] Found 8262 probes; probeID range is [141577-149839]
[RUNNING: chr16] Calculating median RPKM
[RUNNING: chr16] Masking 225 probes with median RPKM < 1.000000
[RUNNING: chr16] Calculating ZRPKM scores...
[RUNNING: chr16] SVD decomposition...
[RUNNING: chr16] Saving SVD-ZRPKM values
[RUNNING: chr17] Now on: chr17
[RUNNING: chr17] Found 11596 probes; probeID range is [149839-161435]
[RUNNING: chr17] Calculating median RPKM
[RUNNING: chr17] Masking 238 probes with median RPKM < 1.000000
[RUNNING: chr17] Calculating ZRPKM scores...
[RUNNING: chr17] SVD decomposition...
[RUNNING: chr17] Saving SVD-ZRPKM values
[RUNNING: chr18] Now on: chr18
[RUNNING: chr18] Found 2988 probes; probeID range is [161435-164423]
[RUNNING: chr18] Calculating median RPKM
[RUNNING: chr18] Masking 47 probes with median RPKM < 1.000000
[RUNNING: chr18] Calculating ZRPKM scores...
[RUNNING: chr18] SVD decomposition...
[RUNNING: chr18] Saving SVD-ZRPKM values
[RUNNING: chr19] Now on: chr19
[RUNNING: chr19] Found 11162 probes; probeID range is [164423-175585]
[RUNNING: chr19] Calculating median RPKM
[RUNNING: chr19] Masking 338 probes with median RPKM < 1.000000
[RUNNING: chr19] Calculating ZRPKM scores...
[RUNNING: chr19] SVD decomposition...
[RUNNING: chr19] Saving SVD-ZRPKM values
[RUNNING: chr20] Now on: chr20
[RUNNING: chr20] Found 4931 probes; probeID range is [175585-180516]
[RUNNING: chr20] Calculating median RPKM
[RUNNING: chr20] Masking 166 probes with median RPKM < 1.000000
[RUNNING: chr20] Calculating ZRPKM scores...
[RUNNING: chr20] SVD decomposition...
[RUNNING: chr20] Saving SVD-ZRPKM values
[RUNNING: chr21] Now on: chr21
[RUNNING: chr21] Found 2066 probes; probeID range is [180516-182582]
[RUNNING: chr21] Calculating median RPKM
[RUNNING: chr21] Masking 71 probes with median RPKM < 1.000000
[RUNNING: chr21] Calculating ZRPKM scores...
[RUNNING: chr21] SVD decomposition...
[RUNNING: chr21] Saving SVD-ZRPKM values
[RUNNING: chr22] Now on: chr22
[RUNNING: chr22] Found 4159 probes; probeID range is [182582-186741]
[RUNNING: chr22] Calculating median RPKM
[RUNNING: chr22] Masking 134 probes with median RPKM < 1.000000
[RUNNING: chr22] Calculating ZRPKM scores...
[RUNNING: chr22] SVD decomposition...
[RUNNING: chr22] Saving SVD-ZRPKM values
[RUNNING: chr23] Now on: chrX
[RUNNING: chr23] Found 6874 probes; probeID range is [186741-193615]
[RUNNING: chr23] Calculating median RPKM
[RUNNING: chr23] Masking 156 probes with median RPKM < 1.000000
[RUNNING: chr23] Calculating ZRPKM scores...
[RUNNING: chr23] SVD decomposition...
[RUNNING: chr23] Saving SVD-ZRPKM values
[RUNNING: chr24] Now on: chrY
[RUNNING: chr24] Found 465 probes; probeID range is [193615-194080]
[RUNNING: chr24] Calculating median RPKM
[RUNNING: chr24] Masking 158 probes with median RPKM < 1.000000
[RUNNING: chr24] Calculating ZRPKM scores...
[RUNNING: chr24] SVD decomposition...
[RUNNING: chr24] Saving SVD-ZRPKM values
[RUNNING] Saving sampleIDs to file...
[FINISHED]
[user@cn3111 ~]$ exit salloc.exe: Relinquishing job allocation 46116226 [user@biowulf ~]$