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# How to get deletions?

Member Posts: 13

Dear GATK Users,

Could anybody tell me how to identify the deletions from the bam file using GATK module??
Actually i used UnifiedGenotyper i am getting list like

# CHROM POS ID REF ALT QUAL FILTER INFO FORMAT human

gi|262 48155 . G A 80.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.103;DP=10;Dels=0.00;FS=0.000;HaplotypeScore

Thanks
Sridhar

Tagged:

• Member Posts: 68 ✭✭✭

If using UnifiedGenotyper you need to make sure you add the option -glm BOTH to call both SNPs and Indels or -glm INDEL just to call indels. If your only working with a few samples you really should use the GATK HaplotypeCaller for calling Indels.

In a VCF a 6 base Insertion looks something like:

gi|262      48155     .     G       GACTGAT      80.77 . AC=1;...

while a deletion looks like:

gi|262      48155     .     GACACTGG      .    80.77 . AC=1;...`

To make them easier to spot you can add a variant Type value (SNP,INS,DEL etc) to the INFO line using SNPEFF's SnpSift tool. There may also be a tool to do that with GATK.

Yes, there is a variant type annotation; see the documentation for usage.

Geraldine Van der Auwera, PhD

• Member Posts: 13

Thank for the reply aeonism , Geraldine,

is it necessary to use dbSNP.vcf file while running UnifiedGenotyper or Variant Annotator??
because i am getting error while using the dbSNP file which i downloaded from (ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/VCF/00-All.vcf.gz)

##### ERROR reference contigs = [gi|262359905|ref|NG_005905.2|]

No, it's not necessary, but it can be informative.

The error you are getting is because you used a version of dbsnp that is not compatible with the reference you are using. It looks like you are using a custom reference, not one of the standard human ones, is that correct?

Geraldine Van der Auwera, PhD

• Member Posts: 13

Hello Geraldine,