bgm-cwg / novocaller Goto Github PK

Hi,

When trying to run the python script using the bam files and the output of step one, I get this error:
Traceback (most recent call last):
File "/nfs/projects/refractory_epilepsy/Novocaller_test/novoCaller/novoCallerBAM.py", line 802, in
runner(outfilename,initial_filename,unrelated_filename,trio_filename)
File "/nfs/projects/refractory_epilepsy/Novocaller_test/novoCaller/novoCallerBAM.py", line 731, in runner
PP,ADfs,ADrs,ADfs_U,ADrs_U,rho_f_new,rho_r_new,prior_L_new,AF_unrel = PP_calc(trio_samfiles,unrelated_samfiles,chrom,pos,REF,ALT,allele_freq,MQ_thresh,BQ_thresh)
File "/nfs/projects/refractory_epilepsy/Novocaller_test/novoCaller/novoCallerBAM.py", line 628, in PP_calc
ADfs,ADrs = get_all_ADs_combined(unrelated_samfiles,chrom,pos,REF,ALT,MQ_thresh,BQ_thresh)
File "/nfs/projects/refractory_epilepsy/Novocaller_test/novoCaller/novoCallerBAM.py", line 312, in get_all_ADs_combined
ADf,ADr = get_ADs_combined(samfile,chrom,position_actual,REF,ALT,MQ_thresh,BQ_thresh)
File "/nfs/projects/refractory_epilepsy/Novocaller_test/novoCaller/novoCallerBAM.py", line 303, in get_ADs_combined
ADf,ADr = get_ADs(samfile,chrom,position_actual,REF[0],MQ_thresh,BQ_thresh)
File "/nfs/projects/refractory_epilepsy/Novocaller_test/novoCaller/novoCallerBAM.py", line 149, in get_ADs
SP=samfile.pileup("chr"+CC, position, position+1)
File "pysam/libcalignmentfile.pyx", line 1326, in pysam.libcalignmentfile.AlignmentFile.pileup
File "pysam/libchtslib.pyx", line 685, in pysam.libchtslib.HTSFile.parse_region
ValueError: invalid contig chr1

Hi developers of novoCaller,

I have tried running the first layer of novoCaller with the following command but the program just keep on running for over 24 hours without generating any output data. I am new to bioinformatics so please correct me if I made any mistakes.

Command:
novoCaller -I input.vcf -O step_1_out.txt -T sample_id.txt -X 1 -P 0.005 -E 0.008

vcf:
example.vcf.gz

sample ID file:
sample_id.txt

It would be very helpful if you can provide example files for the program.

Thanks a lot!

Marcus

seems I put this question on the wrong page. sorry, I should put it at here; https://github.com/dbmi-bgm/granite, but I cannot find the issues button on the granite page...

Hi, i have some questions when i using novocaller, maybe someone can help me figure out some of these:

1. Can novo caller detect de novo indel?
2. when calling DNVs, the unrelated files refer to a) independent trios from the specific trios; b) samples with unrelated phenotypes that not suppose to carry DNV in this position; 3) samples that are independent of each other and the specific trios.
3. how many un-related samples will novoCaller prefer
4. we know sequencing error and gatk may detect more than one DNVs in many trios at an identical position, which is not a real DNV but a sequencing error, in case I used many other trios as un-related samples and the error DNVs in other trios at this position will increase or decrease the DNV probability
5. I saw the example vcf file, is it necessary to put the child at the first genotype column [10th column in vcf file]. the reason I ask this question is because I have many trios, if it is necessary to put the child in the 10th column in vcf file, that means I have to create many big vcf files containing similar un-related samples for each trio