I'm running Dindel 1.01 on bam files produced by BWA and Stampy, looking for small indels. All the steps run to completion but every candidate indel encounters an error, so the final vcf file is completely empty. The errors are the following (output from cat *.glf.txt | grep "chr" | cut -d " " -f 1 | sort | uniq -c):
These proportions are typical of all runs I do - "error_too_few_reads" is dominating, though I highly doubt that there are actually too few reads - my coverage is ~25x, and through samtools pileup and manual inspection I know that there are plenty of indels that are well covered.
When I run the "getCIGARindels" step, I get some alarming messages printed to stdout:
I get about ~20 of these "faidx error" in a typical run (though not for every chromosome). I can't find anything wrong with my reference genome file or it's index file (indexed using samtools faidx - appended at end of post). I don't know if these errors are related to the above ones.
My commands (running on 64bit Ubuntu):
My fasta.fai file:
Code:
14 error_above_read_count_threshold 3 error_Cannot_find_reference_sequence. 598 error_too_few_reads
When I run the "getCIGARindels" step, I get some alarming messages printed to stdout:
Code:
Parsing indels from CIGAR strings... Wrote indels in CIGARS for target chr1 to file candidate_dindels Wrote indels in CIGARS for target chr2 to file candidate_dindels error: faidx error, len==0 start: -24 end: error: faidx error, len==0 start: -11 end:
My commands (running on 64bit Ubuntu):
Code:
dindel-1.01-linux-64bit --analysis getCIGARindels --bamFile input.bam --outputFile candidate_dindels --ref ref_genome.fasta python makeWindows.py --inputVarFile candidate_dindels.variants.txt --windowFilePrefix realign_windows --numWindowsPerFile 2000 dindel-1.01-linux-64bit --analysis indels --bamFile input.bam --ref ref_genome.fasta --libFile candidate_dindels.libraries.txt --varFile $infile --outputFile $outfile
Code:
chr1 230208 6 100 101 chr2 813178 232523 100 101 chr3 316617 1053839 100 101 chr4 1531919 1373629 100 101 chr5 576869 2920874 100 101 chr6 270148 3503518 100 101 chr7 1090947 3776374 100 101 chr8 562643 4878237 100 101 chr9 439885 5446513 100 101 chr10 745741 5890804 100 101 chr11 666454 6644010 100 101 chr12 1078175 7317136 100 101 chr13 924429 8406100 100 101 chr14 784334 9339781 100 101 chr15 1091289 10131966 100 101 chr16 948062 11234175 100 101 chr17 85779 12191725 100 101 chr18 6318 12278369 100 101
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