anahama

I found out that the issue was with using the vcf file of varscan output. From the example on bam-readcount, I realized that the variants should be in bed file. After converting to bed file, the program is now working; however, all the output is with 0 values, and constant message "could not find single-end mapping quality." I really think that the bam-readcount needs to be revamped and improved, to fix all different issues with compilation, file acceptance, and even the single-end vs paired-end...

Hi, I’m having some issues with running the bam-readcount for trio analysis. After checking the article about VarScan I could finally find out that the proper syntax of the order would be bam-readcount -q 1 -b 20 -f [ref.fasta] -l [varscan.variatnts.file] [child-bam-file] > varscan.variant.readcount When I ran the script for the first time, I got an error of (Bam index could not be found), although it was actually there, I deleted the index file and recreated another index using samtools. Now everytime...

Hi, I’m having some issues with running the bam-readcount for trio analysis. After checking the article about VarScan I could finally find out that the proper syntax of the order would be bam-readcount -q 1 -b 20 -f [ref.fasta] -l [varscan.variatnts.file] [child-bam-file] > varscan.variant.readcount When I ran the script for the first time, I got an error of (Bam index not found), although it was actually there, I deleted the index file and recreated another index using samtools. Now everytime I...

Hi, I’m having some issues with running the bam-readcount for trio analysis. After checking the article about VarScan I could finally find out that the proper syntax of the order would be bam-readcount -q 1 -b 20 -f [ref.fasta] -l [varscan.variatnts.file] [child-bam-file] > varscan.variant.readcount When I ran the script for the first time, I got an error of (Bam index could not be found), although it was actually there, I deleted the index file and recreated another index using samtools. Now everytime...