I'm having problem running Pindel0.2.4 to call variants in the exome data.
1) I prepare the configuration txt file.
/path to/sample_sorted_rmpcrdup.bam 300 sample_name
2) I tried running pindel.
"pindel -f ref.fasta -i conf.txt -c ALL -o prefix"
3) i always get the results for only chr1, for chr2 (and after (chr2,3,4,....)) was no result.
No currentState.Reads for chr2 found in /path to/sample_sorted_rmpcrdup.bam
BAM file index 0 0
There are no reads for this bin.
4) Then, I tried running pindel only chr2.
"pindel -f ref.fasta -i conf.txt -c chr2 -o prefix"
5) I get the results for chr2 as well as chr1 at -c ALL.
What have i done wrong?
How can i get all chromosome data?
Thanks
1) I prepare the configuration txt file.
/path to/sample_sorted_rmpcrdup.bam 300 sample_name
2) I tried running pindel.
"pindel -f ref.fasta -i conf.txt -c ALL -o prefix"
3) i always get the results for only chr1, for chr2 (and after (chr2,3,4,....)) was no result.
No currentState.Reads for chr2 found in /path to/sample_sorted_rmpcrdup.bam
BAM file index 0 0
There are no reads for this bin.
4) Then, I tried running pindel only chr2.
"pindel -f ref.fasta -i conf.txt -c chr2 -o prefix"
5) I get the results for chr2 as well as chr1 at -c ALL.
What have i done wrong?
How can i get all chromosome data?
Thanks
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