Problem with Pindel output

[vd4mindia]

Hi,

I have been using normal/tumor GATK processed realigned and recalibrate bam files for mutation , indel and CNV analysis. I have used this bam with VarScan, GATK, Lofreq, Mutect and I have extracted outputs from them. Now am trying to find INDELs from my data and I have extracted them with VarScan and Lofreq. I want to try a hand on Pindel as well and I used it for the first time on my exome data. I see that all the files are empty in the output except *_RP which is basically the output for read support information. I checked with my bam file header and also the hg19 index file and are in the same fashion.

Tumor Bam file

@HD    VN:1.0    GO:none    SO:coordinate
@SQ    SN:chrM    LN:16571
@SQ    SN:chr1    LN:249250621
@SQ    SN:chr2    LN:243199373
@SQ    SN:chr3    LN:198022430
@SQ    SN:chr4    LN:191154276
@SQ    SN:chr5    LN:180915260
@SQ    SN:chr6    LN:171115067
@SQ    SN:chr7    LN:159138663
@SQ    SN:chr8    LN:146364022
@SQ    SN:chr9    LN:141213431

Normal bam

@HD    VN:1.0    GO:none    SO:coordinate
@SQ    SN:chrM    LN:16571
@SQ    SN:chr1    LN:249250621
@SQ    SN:chr2    LN:243199373
@SQ    SN:chr3    LN:198022430
@SQ    SN:chr4    LN:191154276
@SQ    SN:chr5    LN:180915260
@SQ    SN:chr6    LN:171115067
@SQ    SN:chr7    LN:159138663
@SQ    SN:chr8    LN:146364022
@SQ    SN:chr9    LN:141213431

hg19 index file

chrM    16571    6    50    51
chr1    249250621    16915    50    51
chr2    243199373    254252555    50    51
chr3    198022430    502315922    50    51
chr4    191154276    704298807    50    51
chr5    180915260    899276175    50    51
chr6    171115067    1083809747    50    51
chr7    159138663    1258347122    50    51
chr8    146364022    1420668565    50    51
chr9    141213431    1569959874    50    51

I do not see any difference with the pattern of both ref sequence and my tumor bam file and normal bam file. Both starts with chrM as needed for GATK processing. I calculated the mean insert size for this bam files are well and put them in the config file and ran the command but during the run it adds BD values to some and most of the time it does not show any read pairs. I do not see any output in any of the output files except for the *_RP files. Below are is an example of config file I used and the command I used to run the Pindel tool.

config.txt

T_S7998.realigned.recal.bam 211 TUMOR_HG
N_S8980.realigned.recal.bam 187 NORMAL_HG

Command

../pindel -f hg19/hg19.fa -i config/S_313_tumor_config.txt -c ALL -o /pindel_out/results/S_313_T_pindel

Output

-rw-r--r-- 1 vdas DPT      0 Mar  4 18:47 S_313_T_pindel_SI
-rw-r--r-- 1 vdas DPT      0 Mar  4 18:47 S_313_T_pindel_D
-rw-r--r-- 1 vdas DPT      0 Mar  4 18:47 S_313_T_pindel_TD
-rw-r--r-- 1 vdas DPT      0 Mar  4 18:47 S_313_T_pindel_INV
-rw-r--r-- 1 vdas DPT      0 Mar  4 18:47 S_313_T_pindel_LI
-rw-r--r-- 1 vdas DPT      0 Mar  4 18:47 S_313_T_pindel_BP
-rw-r--r-- 1 vdas DPT      0 Mar  4 18:47 S_313_T_pindel_CloseEndMapped
-rw-r--r-- 1 vdas DPT  86651 Mar  4 19:47 S_313_T_pindel_RP

I would like to know where am getting wrong. I already checked in the forum and these problems are usually if the bam and the ref.fai are not in same order but in my case they are same. So I would like to know what is causing the problem in my case. Sorry for such detailed post but I wanted to show that all the stuffs seem ok to me for running the command but still am encountering the problem. I would like some assistance here. I wrote under Pindel tag in Biostars since in your website it was written that support is available at Biostars , but I have received any reply on my post past 4 days. I would appreciate if you can let me know where am getting wrong.