ettwiller / damage-estimator Goto Github PK

HI,

Shouldnt if ($$relative_count_R1{$type}{"total_type"} && $$relative_count_R2{$type}{"total_type"}) be if ($$relative_count_R1{$type}{"total_type"} && $$relative_count_R2{$type_RC}{"total_type"})?

The relative_count_R2{$type} should be the reverse complement, therefore, it should be $$relative_count_R2{$type_RC}{"total_type"}?

Wilson

Hello,

I am trying to calculate GIV scores for a list of somatic variants. I created mpileup files for only the variant base by adding -r option to the samtools mpileup function. I used the -q 20 and -Q 30 and can see the variant in the base reads in the mpileup files.

When I use the estimage_damage.pl script with these mpileup files the outputs are either empty or do not contain a score or any information for the variant (ex. G_T) but rather only for the non variant (ex G_G) evidence. I do not believe the filters are removing the reads with the variant information as the most relaxed filters I used were --qualityscore 10 and the default coverage options.

I would greatly appreciate any advice or suggestions. Please let me know if you need more information.

Thank you!