Pindel BAM File Processing

Question

[arvmanya]

We setup Pindel on our server and after then tried to test it out with BAM files, Cystic fibrosis transmembrane conductance regulator (CFTR) gene. But the output files generated are of size ZERO KB, both for CFTR-1_S2 and CFTR-4_S5 files, (did not use manifest file as that is optional).

Not sure if this is as expected or are we missing something, to get the desired output. Also, we were trying to use manifest file along with Pindel command but did not see any option to use.

CFTR-S1

../pindel -f CFTR_sequence.fasta -i CFTR1config.txt -c ALL -o CFTR_1S2
Initializing parameters...
Pindel version 0.2.5b9, 20160729.
Loading reference genome ...
Loading reference genome done.
Initializing parameters done.
Please use samtools to index your reference file.
.fai is missing.

../pindel -f CFTR_sequence.fasta -i CFTR1config.txt -c ALL -o CFTR_1S2
Initializing parameters...
Pindel version 0.2.5b9, 20160729.
Loading reference genome ...
Loading reference genome done.
Initializing parameters done.
SearchRegion::SearchRegion
Processing region: NG_016465.4:19180-207882      1          188703
Chromosome Size: 188704
NumBoxes: 64785 BoxSize: 12

Looking at chromosome NG_016465.4:19180-207882 bases 1 to 188703 of the bed region: chromosome NG_016465.4:19180-207882:1-188703 
[W::hts_idx_load3] The index file is older than the data file: CFTR-1_S2.bam.bai
[E::sam_itr_next] Null iterator
No discordant RP reads in Bamfile CFTR-1_S2.bam
Discovery RP: 0
sorting RP complete.
Reads_RP.size(): 0
Modify RP complete.
adding BD from RP.
modify and summarize interchr RP.
adding BD from interChr RP.
summarize BP as BD complete. Now start sorting BD...
sorting BD... done.
external BD events: 0 Added BreakDancer-like events: 0

Insertsize in config: 250
[W::hts_idx_load3] The index file is older than the data file: CFTR-1_S2.bam.bai
[E::sam_itr_next] Null iterator
The number of one end mapped read: 0
Number of problematic reads in current window:            0, + 0 - 0
Number of split-reads where the close end could be mapped:  0, + 0 - 0
Percentage of problematic reads with close end mapped:          + 0.00% - 0.00%
No currentState.Reads for NG_016465.4:19180-207882 found in CFTR-1_S2.bam
BAM file index        0
Bam file name        CFTR-1_S2.bam
Number of split-reads so far      0

The number of one end mapped read: 0
There are 0 reads supporting the reference allele.
There are 1 samples.
SampleName2Index done
declaring g_RefCoverageRegion for 1 samples and 188705 positions.
no reads 
InterChromosome_SR.size(): 0
PreviousChrName: 
Initializing pindel 0 seconds.
Loading chromosomes 0 seconds.
Reading in reads + matching close ends 0 seconds.

Could someone please let me know if I am missing something.

[ATpoint]

[W::hts_idx_load3] The index file is older than the data file: CFTR-1_S2.bam.bai

I would start by working on this error message => delete old index, make a new one.

[arvmanya]

Thanks for the response ATpoint I did try that but still same response, that warning is not there now.

../pindel -f CFTR_sequence.fasta -i CFTR1config.txt -c ALL -o CFTR_1S2
Initializing parameters...
Pindel version 0.2.5b9, 20160729.
Loading reference genome ...
Loading reference genome done.
Initializing parameters done.
SearchRegion::SearchRegion
Processing region: NG_016465.4:19180-207882 1   188703
Chromosome Size: 188704
NumBoxes: 64785 BoxSize: 12

Looking at chromosome NG_016465.4:19180-207882 bases 1 to 188703 of the bed region: chromosome NG_016465.4:19180-207882:1-188703 
[E::sam_itr_next] Null iterator
No discordant RP reads in Bamfile CFTR-1_S2.bam
Discovery RP: 0
sorting RP complete.
Reads_RP.size(): 0
Modify RP complete.
adding BD from RP.
modify and summarize interchr RP.
adding BD from interChr RP.
summarize BP as BD complete. Now start sorting BD...
sorting BD... done.
external BD events: 0 Added BreakDancer-like events: 0

Insertsize in config: 250
[E::sam_itr_next] Null iterator
The number of one end mapped read: 0
Number of problematic reads in current window:              0, + 0 - 0
Number of split-reads where the close end could be mapped:  0, + 0 - 0
Percentage of problematic reads with close end mapped:      + 0.00% - 0.00%
No currentState.Reads for NG_016465.4:19180-207882 found in CFTR-1_S2.bam
BAM file index  0
Bam file name   CFTR-1_S2.bam
Number of split-reads so far    0

The number of one end mapped read: 0
There are 0 reads supporting the reference allele.
There are 1 samples.
SampleName2Index done
declaring g_RefCoverageRegion for 1 samples and 188705 positions.
no reads 
InterChromosome_SR.size(): 0
PreviousChrName: 
Initializing pindel 0 seconds.
Loading chromosomes 0 seconds.
Reading in reads + matching close ends 0 seconds.

Answer 1

[ATpoint]

No discordant RP reads in Bamfile CFTR-1_S2.bam

Looks like there are simply no reads indicating a variant.