Understanding glf format (Dindel)
Hi, I used the Dindel (Illumina data), but I had some problems.
In the last step I got a VCF file empty. I am wondering if the filtration criteria in the final step was very strict and I did not have any result (indels), or if there is some problem in my glf files.
There is no information about the meaning of each of the columns of the glf files (in the manual, paper or in the internet). I used the options for pooled samples (I have a pool of 10 individuals in 1 bam file).
For example (one of my glf file)
msg index analysis_type tid lpos rpos center_position realigned_position was_candidate_in_window ref_all nref_all num_reads post_prob_variant qual est_freq logZ hapfreqs indidx msq numOffAll num_indel num_cover_forward num_cover_reverse num_unmapped_realigned var_coverage_forward var_coverage_reverse nBQT nmmBQT mLogBQ nMMLeft nMMRight glf
ok 1 singlevariant Chr26 3187 3306 3246 3247 1 NA +C 21 9.98874e-05 NA 4.77032e-09 -223.375 REF:1 0 31.5851 NA NA 1 0 0 0 0 NA NA NA NA NA 0/0:-223.378;0/1:-224.072;1/1:-231.078
ok 2 singlevariant Chr26 5249 5370 5309 5309 1 NA -TC 33 9.98882e-05 NA 3.03579e-09 -230.288 REF:1 0 47.8989 NA NA 0 0 0 0 0 NA NA NA NA NA 0/0:-230.291;0/1:-240.792;1/1:-398.575
ok 3 singlevariant Chr26 5466 5585 5525 5526 1 NA +C 46 9.98788e-05 NA 2.17551e-09 -461.289 REF:1 0 40.4144 NA NA 0 2 0 1 1 NA NA NA NA NA 0/0:-461.291;0/1:-465.257;1/1:-542.35
Questions
1) In my interpretation the quality score (phred score) is the "qual", is it correct? Because this is one of the criteria selection and in this column I got only "NA".
2)"num_indel" is the number of indels that I got? because I had only "NA" again..
3) "est_freq" is the allele frequency of the indel?
4) What is the "msq"?
5) "rpos" is the position in the reference sequence or in the realigned sequence?
6) What is "lpos"?
7) What is important to check in these columns?
8) What is the last column?
Someone could help me? Thanks
In the last step I got a VCF file empty. I am wondering if the filtration criteria in the final step was very strict and I did not have any result (indels), or if there is some problem in my glf files.
There is no information about the meaning of each of the columns of the glf files (in the manual, paper or in the internet). I used the options for pooled samples (I have a pool of 10 individuals in 1 bam file).
For example (one of my glf file)
msg index analysis_type tid lpos rpos center_position realigned_position was_candidate_in_window ref_all nref_all num_reads post_prob_variant qual est_freq logZ hapfreqs indidx msq numOffAll num_indel num_cover_forward num_cover_reverse num_unmapped_realigned var_coverage_forward var_coverage_reverse nBQT nmmBQT mLogBQ nMMLeft nMMRight glf
ok 1 singlevariant Chr26 3187 3306 3246 3247 1 NA +C 21 9.98874e-05 NA 4.77032e-09 -223.375 REF:1 0 31.5851 NA NA 1 0 0 0 0 NA NA NA NA NA 0/0:-223.378;0/1:-224.072;1/1:-231.078
ok 2 singlevariant Chr26 5249 5370 5309 5309 1 NA -TC 33 9.98882e-05 NA 3.03579e-09 -230.288 REF:1 0 47.8989 NA NA 0 0 0 0 0 NA NA NA NA NA 0/0:-230.291;0/1:-240.792;1/1:-398.575
ok 3 singlevariant Chr26 5466 5585 5525 5526 1 NA +C 46 9.98788e-05 NA 2.17551e-09 -461.289 REF:1 0 40.4144 NA NA 0 2 0 1 1 NA NA NA NA NA 0/0:-461.291;0/1:-465.257;1/1:-542.35
Questions
1) In my interpretation the quality score (phred score) is the "qual", is it correct? Because this is one of the criteria selection and in this column I got only "NA".
2)"num_indel" is the number of indels that I got? because I had only "NA" again..
3) "est_freq" is the allele frequency of the indel?
4) What is the "msq"?
5) "rpos" is the position in the reference sequence or in the realigned sequence?
6) What is "lpos"?
7) What is important to check in these columns?
8) What is the last column?
Someone could help me? Thanks