Pindel output Row 32+ per sample details

[millerrruth]

Hi,
I am running Pindel on some Illumina data.
I am having trouble interpreting the final "per sample" columns of the output files.
The manual (http://gmt.genome.wustl.edu/pindel/0...er-manual.html) says that lines 32+ are "Per sample" and consist of the sample id, plus 4 values for each sample (ie. the sample name, followed by the total number of supporting reads whose anchors are upstream, the total number of unique supporting reads whose anchors are upstream, the total number of supporting reads whose anchors are downstream, and finally the total number of unique supporting reads whose anchors are downstream.)
However in my output I get 6 values following every sample name. (eg:
C9343 5 5 12 10 1 1)
Can you please explain what these extra 2 values are, and the order of the values.

Thanks,

Ruth

[KaiYe]

Hi,
I am running Pindel on some Illumina data.
I am having trouble interpreting the final "per sample" columns of the output files.
The manual (http://gmt.genome.wustl.edu/pindel/0...er-manual.html) says that lines 32+ are "Per sample" and consist of the sample id, plus 4 values for each sample (ie. the sample name, followed by the total number of supporting reads whose anchors are upstream, the total number of unique supporting reads whose anchors are upstream, the total number of supporting reads whose anchors are downstream, and finally the total number of unique supporting reads whose anchors are downstream.)
However in my output I get 6 values following every sample name. (eg:
C9343 5 5 12 10 1 1)
Can you please explain what these extra 2 values are, and the order of the values.

Thanks,

Ruth

SampleID RefSupportingLeft RefSupportingRight AltSupportingLeft AltSupportingLeftUnique AltSupportingRight AltSupportingRightUnique

[millerrruth]

Hi,
Thanks.
So to clarify RefSupportingLeft and RefSupportingRight are the number of reads that support the reference sequence, and therefore not the variant?
Whereas Alt... are the number of reads that support the variant as documented in the rest of the row?
Ruth

[KaiYe]

Hi,
Thanks.
So to clarify RefSupportingLeft and RefSupportingRight are the number of reads that support the reference sequence, and therefore not the variant?
Whereas Alt... are the number of reads that support the variant as documented in the rest of the row?
Ruth

Ref = reference allele
Alt = variant allele

take max(RefSupportingLeft, RefSupportingRight) and sum(AltSupportingLeft, AltSupportingRight) for your genotype. if you run pindel2vcf, this should be take cared already.