teststrandbias problem

[srx3001]

Hello,
I am testing VarDict on the sample files provided (my.bam and my.bed) and I always get an empty output.
The command I use is:

AF_THR="0.01"
vardict -G /mnt/Homo_sapiens.GRCh37.dna.primary_assembly.fa -f $AF_THR -N TP53 -b my.bam -c 1 -S 2 -E 3 -g 4 my.bed | teststrandbias.R | var2vcf_valid.pl -N TP53 -E -f $AF_THR

The error I get is:
Error: Incorrect input detected in teststrandbias.R
Execution halted

When I try to write the output to a file from vardict as so:

vardict -G /mnt/Homo_sapiens.GRCh37.dna.primary_assembly.fa -f $AF_THR -N TP53 -b my.bam -c 1 -S 2 -E 3 -g 4 my.bed > whatever.txt

I get a file with 36 columns and apparently teststrandbias expects 34 or 38. (ill upload it).
whatever.txt

How come this happens?
What are the steps I can take to solve this? Is it because your reference is different?

Thank you in advance,
Srdjan

[PolinaBevad]

@srx3001, hello!
Sorry about this issue!
There are now 36 columns in the simple mode of Vardict (2 columns were added for SV analysis and duprate). We will fix the scripts soon, for now you can change condition in teststrandbias.R from (mynumcols == 34 || mynumcols == 38) to (mynumcols == 36 || mynumcols == 38). Columns for the amplicon mode are the same as before.

[dattam]

@srx3001, hello!
Sorry about this issue!
There are now 36 columns in the simple mode of Vardict (2 columns were added for SV analysis and duprate). We will fix the scripts soon, for now you can change condition in teststrandbias.R from (mynumcols == 34 || mynumcols == 38) to (mynumcols == 36 || mynumcols == 38). Columns for the amplicon mode are the same as before.

@PolinaBevad , the R script uses the following colClasses, but they don't match the (36 column output). Also, I suppose this incompatibility will also create issues with var2vcf_valid.pl. Do you have any suggestions for a short term fix. Maybe I can "cut" specific columns and feed it to these scripts ? In that case, is there a way to identify the "older" list of columns in the new output ? Thanks!

colClasses=c("character", NA, NA, NA, NA, "character", "character", NA,
NA, NA, NA, NA, NA, "character", NA, NA, NA, NA, NA, NA, NA, NA).