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Unified genotyper give me low DP but i have more than 2000X. Using amplicon data.

Unified/haplotype genotiper reports variants with a very low DP, But i m working with amplicons and i have more tan 3000X in that areas.
I didnt mark duplicates, and not using any filter. I had validated the bam file with picard and it is ok.
I use PrintReads -rf with all posible filters and only MateSamStrand and NoOriginalQualityScore can filter something but i dont use it and it is suppose UG neither internaly.

Lines in my vcf looks like:

chr1 27505535 . A G 30.74 LowQual AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=70.00;MQ0=0;QD=15.37 GT:AD:DP:GQ:PL 1/1:0,2:2:6:58,6,0
chr1 29161609 rs2236857 T C 17.61 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=70.00;MQ0=0;QD=8.80 GT:AD:DP:GQ:PL 1/1:0,2:2:3:44,3,0
chr1 29292131 . C G 55.28 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.727;DP=4;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=70.00;MQ0=0;MQRankSum=-0.727;QD=13.82;ReadPosRankSum=-0.727 GT:AD:DP:GQ:PL 1/1:1,3:4:9:83,9,0
chr1 30219578 rs142792281 C T 30.74 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=62.95;MQ0=0;QD=15.37 GT:AD:DP:GQ:PL 1/1:0,2:2:6:58,6,0

I test haplotype option but i have the same problem, even i get variants with DP=0

chr15 20495000 . G A 2607.77 . AC=2;AF=1.00;AN=2;DP=0;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=0.00;MQ0=0 GT:GQ:PL 1/1:99:2636,178,0
chr15 27741558 . CT C 54.52 . AC=2;AF=1.00;AN=2;DP=0;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=0.00;MQ0=0 GT:GQ:PL 1/1:7:91,7,0

This is another question, what it is posible?
In short ¿why the DP asociated to variants is less than 10 when i have more than 1000X?Is like anly diferent reads (due the clippings effects) are taken in acount but i can ensure that and i dont know what can more i can test. ¿What is the solution to consider all my reads?

Thanks a lot.
Best regards.

David de Una.

Answers

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