Closed ShixiangWang closed 7 months ago
I checked the paired tumor. It seems the issue is caused by the SAM flag. I am a newbie to this. Is it possible to keep them all without considering SAM flag?
$ alleleCounter -l test.loc -b ~/data/gdc/wes/TCGA-AA-3869-01A-01W-0995-10_hg19_Illumina_gdc_realn.bam -o test.txt
[W::hts_idx_load2] The index file is older than the data file: /public/home/zhaoqi/data/gdc/wes/TCGA-AA-3869-01A-01W-0995-10_hg19_Illumina_gdc_realn.bai
Reading locis
Done reading locis
$ cat test.txt
#CHR POS Count_A Count_C Count_G Count_T Good_depth
chr3 58125556 0 385 0 0 385
chr3 58125557 0 0 353 1 354
chr3 58125558 0 1 0 401 402
chr3 58125559 0 0 0 405 405
chr3 58125560 0 0 0 398 398
alleleCount is intended to be used on primary mappings of paired-end sequencing. The example you provided has all reads indicated as unpaired (no flag bit 1) and many are PCR/optical duplicates which you would not want to count (useful tool).
The tool could be extended to support unpaired data, but it will be at the discretion of our internal priorities.
@keiranmraine Thanks for your response. It's strange that this is a normal sample bam downloaded from GDC portal. This indicates the the sample quality is bad and should be not used in my analysis.
It would be nice if the program can print a message when no paired reads found or summarize how many reads filtered out so the result is more readable in such cases.
Thanks again. And I have no questions further.
Shixiang
Hi @ShixiangWang and @keiranmraine
I have the same problem (only zeros in my allele count output). I am using bam files from paired-end sequencing. I am using version 4.3.0 of alleleCounter. I found the problem while running Battenberg, but the output is the same even when I am using alleleCounter by its self.
#CHR POS Count_A Count_C Count_G Count_T Good_depth
1 16103 0 0 0 0 0
1 51479 0 0 0 0 0
1 51898 0 0 0 0 0
1 51928 0 0 0 0 0
1 54490 0 0 0 0 0
1 54708 0 0 0 0 0
1 54716 0 0 0 0 0
1 54753 0 0 0 0 0
1 55299 0 0 0 0 0
Thankful for any help on how to solve this!
@a3schiller I am no longer involved in the support of this tool. @AndyMenzies may be able to delegate someone to help.
Thakns for your fast reply and delegating the question!
@AndyMenzies, I am thankful for any help on how to solve this!
@a3schiller I too am no longer on this project, however, a few useful things to provide would be:
samtools view -c -f 3 -F 3852 your_file.bam 1:1-n
An update if anyone is having the same problem in the future.
The problem was that I used an loci-file without chr-prefix but an BAM-file with chr-index. Using an loci-file with chr-index made it work for me!
Thanks for the update. I've fallen for that GRCh37 -> GRCh38 trap before. Glad you got it working.
Hi developers,
Thanks for developing this tool. I have questions when I use this tool. I found I cannot count any allele in a bam file, even with
-m 0 -q 0
. However, I found the bam file has nothing wrong. Below is an example.Why this happen? Any suggestions?
Best,
Shixiang