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dariober / cnv_facets

Somatic copy variant caller (CNV) for next generation sequencing
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Closed stroke1989 closed 2 years ago

stroke1989 commented 2 years ago

Hi, I'm a new to facets, Thanks for this excellent tool. When I use this tool to analysis cnv. EORROR occurred:

facets

the vcf and bam file have the same chromosome name, so I don't think is the chromosome caused this proble. I need your help. Hope your response! Appreciate!

dariober commented 2 years ago

Hi- If you can upload a small portion of the input files to something like dropbox, I'll try to have a look at what's happening. I assume your bam files have acceptable mapping and base quality so that not every read gets discarded?

stroke1989 commented 2 years ago

Hi- If you can upload a small portion of the input files to something like dropbox, I'll try to have a look at what's happening. I assume your bam files have acceptable mapping and base quality so that not every read gets discarded?

https://www.dropbox.com/t/N8XObj3LgB4OAymf this is the dropbox link, you can download the bam and commnon_all file. Hope your response.

stroke1989 commented 2 years ago

@dariober Hi, I tried again and failed again, the error is similar to the 1st time. could you tell me how to solve this problem?Hope your reponse! Appreciate!

dariober commented 2 years ago

@stroke1989 - By now, you may have found out what the issue is here... The problem is that you aligned your fastq fies using the first-in-pair read twice. In the header of one of the files I see (slightly edited):

@PG     ID:bwa  PN:bwa  VN:0.7.17-r1188 CL:bwa mem -t 8 -M [...] SCA_876_N_clean_R1.fastq.gz SCA_876_N_clean_R1.fastq.gz

Almost for sure the second file should be SCA_876_N_clean_R2.fastq.gz.

This mistake makes all the alignment anomalous because both reads in a "pair" align to the same strand. snp-pileup, one of the components of cnv_facets.R, discards such alignment and you are left with no alignments, hence the error you see.

For the record, you can include anomalous read pairs with the option --snp-count-orphans/-A but in this case almost for sure you want to fix the bam files.

stroke1989 commented 2 years ago

@stroke1989 - By now, you may have found out what the issue is here... The problem is that you aligned your fastq fies using the first-in-pair read twice. In the header of one of the files I see (slightly edited):

@PG     ID:bwa  PN:bwa  VN:0.7.17-r1188 CL:bwa mem -t 8 -M [...] SCA_876_N_clean_R1.fastq.gz SCA_876_N_clean_R1.fastq.gz

Almost for sure the second file should be SCA_876_N_clean_R2.fastq.gz.

This mistake makes all the alignment anomalous because both reads in a "pair" align to the same strand. snp-pileup, one of the components of cnv_facets.R, discards such alignment and you are left with no alignments, hence the error you see.

For the record, you can include anomalous read pairs with the option --snp-count-orphans/-A but in this case almost for sure you want to fix the bam files.

Thanks very much. Appreciate! Finallly, as you pointed out, this issue was resolved