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I ran ./extract_duplicates to estimate PCR duplication rate on our data:
./extract_duplicates --bam SRR1585519.dedup.merged.sorted.bam --VCF NA19099.het.vcf --mmq 20 > SRR1585519.dedup.hetreads
however it returned:
PCR duplicates marked 0 total-reads 0 frac nan discarded 62152388
#clusters
total reads (PE=1) 0 unique-reads 0 duplicates:0, duplication rate nan
Using samtool rmdup and IGV, we observed a lot of duplicate reads in our data, but the script here seemed to not work on our files. What's the problem here?
The text was updated successfully, but these errors were encountered:
I did add "--singlereads 1" in our command line, but the output was still the same.
I ran the script on another input file (PE reads) and did get the output file. So there is an issue of the script to take a SE file as an input.
However, when I ran the next script ./estimate_PCRduprate.py I got this output:
identified 0 het variants filtered 0 high-cov 1e-07 0.0 0.0 0.0
Traceback (most recent call last):
File "estimate_PCRduprate.py", line 407, in
[Frate,Ftotal,Funique,Funiqlist] = calculate_values(duplicate_counts,cluster_counts);
File "estimate_PCRduprate.py", line 103, in calculate_values
p = float(AB_counts[0])/(AB_counts[0] + AB_counts[1]);
ZeroDivisionError: float division by zero
I ran ./extract_duplicates to estimate PCR duplication rate on our data:
./extract_duplicates --bam SRR1585519.dedup.merged.sorted.bam --VCF NA19099.het.vcf --mmq 20 > SRR1585519.dedup.hetreads
however it returned:
PCR duplicates marked 0 total-reads 0 frac nan discarded 62152388
#clusters
total reads (PE=1) 0 unique-reads 0 duplicates:0, duplication rate nan
Using samtool rmdup and IGV, we observed a lot of duplicate reads in our data, but the script here seemed to not work on our files. What's the problem here?
The text was updated successfully, but these errors were encountered: