Open chatterjee89 opened 3 years ago
@akdess I think I may have figured out both the problems (first one is explained within the source code for main.cpp). But I need a solution for the second one.
I think BAFExtract is only pulling/writing for chromosome 4 because it is the only integer in the lot - fly chromosomes are written as 2L, 2R, 3L, 3R, X, Y and 4 and so there's an issue with detection or with writing somewhere. Am I wrong to assume so? Could you please help me fix this issue?
Regards, Deep
Hi,
Thanks for making this wonderful tool! I have run into an issue:
After running the following command...
samtools view ./WT_96_2.bam | BAFExtract -generate_compressed_pileup_per_SAM stdin ./CaSpER/dm6.list ./CaSpER/baf/wt96_2 50 0; BAFExtract -get_SNVs_per_pileup ./CaSpER/dm6.list ./CaSpER/baf/wt96_2 ./CaSpER/dm6_fasta_pileup/ 20 4 0.1 ./CaSpER/baf/wt96_2/WT_96_2.baf
...I get the following std output:
Question 1: what does the 20 4 0.1 parameter for BAFExtract -get_SNVs_per_pileup mean?
It seems to have worked and I can see the .baf file along with the allele_counts.bin files for each chromosome in the output folder. This is the output:
HOWEVER, given that dm6 (fruit-flies) has 2L, 2R, 3L, 3R, 4, X, Y chromosomes, and that the generated baf file only ends up containing the values for chromosome 4, I don't quite understand what happened there. So, Question 2: How can I fix this?
This is for every sample run for the overall experiment. Any help would be greatly appreciated!
Regards, Deep