need some information of using th fpfilter.pl for using it on INDELs vcf file of VarScan output?

[chris.cornor]

Hi,
I am trying to run fpfilter.pl on INDEL out vcf file of varscan. But when am running the command of fpfilter I do not see any output. I am using the bam-readcount command on the tumor bam since my indel vcf's are all somatic. Can you please let me know where am getting wrong and what should I do to avoid the error and get a desired output.

perl -ane 'print join("\t",@F[0,1,1])."\n" unless(m/^#/)' S_313_T_soma_vcf.output.indel.Somatic.hc.vcf > fpfilter/S_313_T_soma_varscan_indels_vcf.var

Given tumor.bam, a BAM file containing the SNVs, and its reference FASTA grch37.fa, run bam-readcount:

bam-readcount -q1 -b15 -w1 -l fpfilter/S_313_T_soma_varscan_indels_vcf.var -f /hg19/hg19.fa /align_files/T_S7998/T_S7998.realigned.recal.bam > fpfilter/S_313_T_soma_varscan_indels_vcf.readcount

Run the fpfilter.pl script using the readcounts as an input:

perl fpfilter.pl S_313_T_soma_vcf.output.indel.Somatic.hc.vcf fpfilter/S_313_T_soma_varscan_indels_vcf.readcount −−output−basename out_HG

Below is the error am receiving:
perl: warning: Falling back to the standard locale ("C").
Use of uninitialized value $ref in uc at /scratch/GT/softwares/fpfilter.pl line 138, <GEN1> line 1.
Use of uninitialized value $var in uc at /scratch/GT/softwares/fpfilter.pl line 139, <GEN1> line 1.
Use of uninitialized value $position in concatenation (.) or string at /scratch/GT/softwares/fpfilter.pl line 147, <GEN1> line 1.
Use of uninitialized value $ref in uc at /scratch/GT/softwares/fpfilter.pl line 138, <GEN1> line 2.
Use of uninitialized value $var in uc at /scratch/GT/softwares/fpfilter.pl line 139, <GEN1> line 2.
Use of uninitialized value $position in concatenation (.) or string at /scratch/GT/softwares/fpfilter.pl line 147, <GEN1> line 2.
Use of uninitialized value $ref in uc at /scratch/GT/softwares/fpfilter.pl line 138, <GEN1> line 3.
Use of uninitialized value $var in uc at /scratch/GT/softwares/fpfilter.pl line 139, <GEN1> line 3.
Use of uninitialized value $position in concatenation (.) or string at /scratch/GT/softwares/fpfilter.pl line 147, <GEN1> line 3.
Use of uninitialized value $ref in uc at /scratch/GT/softwares/fpfilter.pl line 138, <GEN1> line 4.
Use of uninitialized value $var in uc at /scratch/GT/softwares/fpfilter.pl line 139, <GEN1> line 4.
Use of uninitialized value $position in concatenation (.) or string at /scratch/GT/softwares/fpfilter.pl line 147, <GEN1> line 4.
Use of uninitialized value $ref in uc at /scratch/GT/softwares/fpfilter.pl line 138, <GEN1> line 5.
Use of uninitialized value $var in uc at /scratch/GT/softwares/fpfilter.pl line 139, <GEN1> line 5.

368 variants
368 failed to get readcounts for variant allele
0 had read position < 0.1
0 had strandedness < 0.01
0 had var_count < 4
0 had var_freq < 0.05
0 had mismatch qualsum difference > 50
0 had mapping quality difference > 30
0 had read length difference > 25
0 had var_distance_to_3' < 0.2
0 passed the strand filter

I checked the code and it runs with the exception when the vcf file is divided into different arrays for chrom,pos,alt and ref but in varscan2 we have the ID column , is that creating the issue? since the vcf generated with varscan2 is above vcf4.1 while this script does not seems to work for vcf4.1 and above. Is there a new false positive filtering script for INDELS coming from VarScan2 output vcf4.1 files?

I would appreciate your suggestions.