Changes

It is usually useful to examine the call sets against known data sets for the passed variants.

It is usually useful to examine the call sets against known data sets for the passed variants.

 

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If you are running outside the workshop, you will need to update indel.reference.txt to point to the reference files.

''Commands outside of SeqShop Workshop:''

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  cp ${SS}/ref22/indel.reference.txt ${OUT}/indel.reference.txt

  cp ${SS}/ref22/indel.reference.txt ${OUT}/indel.reference.txt

*'''Replace the path to the reference files with the path to your seqshop example directory.'''

*'''Replace the path to the reference files with the path to your seqshop example directory.'''

*:[[File:IndelRef.png]]

*:[[File:IndelRef.png]]

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   data set

   data set

     Sensitivity  69.6%  <br>

     Sensitivity  69.6%  <br>

   dbsnp  #Indels from dbSNP

   dbsnp  #Indels from dbSNP

     A-B        405 [0.68]

     A-B        404 [0.68]

     A&B        208 [0.79]

     A&B        209 [0.79]

     B-A        494 [2.03]

     B-A        493 [2.04]

     Precision    33.9%

     Precision    34.1%

     Sensitivity  29.6%

     Sensitivity  29.8%

Ins/Del ratios:  Reference alignment based methods tend to be biased towards the detection of deletions.  This provides a useful measure for discovery Indel sets to show the varying degree of biasness.  It also appears that as coverage increases, the ins/del ratio tends to 1.

Ins/Del ratios:  Reference alignment based methods tend to be biased towards the detection of deletions.  This provides a useful measure for discovery Indel sets to show the varying degree of biasness.  It also appears that as coverage increases, the ins/del ratio tends to 1.

We perform the same analysis for the failed variants again, the relatively low overlap with known data sets imply a reasonable tradeoff in sensitivity and specificity.

We perform the same analysis for the failed variants again, the relatively low overlap with known data sets imply a reasonable tradeoff in sensitivity and specificity.

   ${GC}/bin/vt profile_indels -g ${OUT}/indel.reference.txt  -r ${SS}/ref22/human.g1k.v37.chr22.fa ${OUT}/final/all.genotypes.vcf.gz -i 22:36000000-37000000 -f  "~PASS"

   ${GC}/bin/vt profile_indels -g ${OUT}/indel.reference.txt  -r ${SS}/ref22/human.g1k.v37.chr22.fa ${OUT}/indel/final/all.genotypes.vcf.gz -i 22:36000000-37000000 -f  "~PASS"

 

   data set

   data set