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
Normal bam
hg19 index file
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
Command
Output
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.
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
Code:
@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
Code:
@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
Code:
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
config.txt
Code:
T_S7998.realigned.recal.bam 211 TUMOR_HG N_S8980.realigned.recal.bam 187 NORMAL_HG
Code:
../pindel -f hg19/hg19.fa -i config/S_313_tumor_config.txt -c ALL -o /pindel_out/results/S_313_T_pindel
Code:
-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