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Forum: Bioinformatics 11-29-2012, 07:51 AM
Replies: 0
Views: 1,957
Posted By nvteja
GATK Haplotype caller missing calls

Hello friends,

I am using GATK Haplotype caller to call snps and indels from a GATK realigned, re-calibrated bam file (following GATK best practices). The only options I have changed from default...
Forum: Bioinformatics 12-09-2010, 08:51 AM
Replies: 1
Views: 3,364
Posted By nvteja
Limit of indel length with bwa

Hi folks,

I am wondering whether there is a limit on maximum size of insertion/deletion inside a read that bwa checks when it is aligning? Like say there should not be a insertion or deletion of...
Forum: Bioinformatics 09-20-2010, 11:15 AM
Replies: 1
Views: 3,707
Posted By nvteja
GATK error

Hi all,

I am trying to use GATK indel realigner to realign indels on one of the bam files. I was able to get the interval file but in the second step when I use by bam file to realign the indels ,...
Forum: Illumina/Solexa 06-28-2010, 09:32 AM
Replies: 2
Views: 7,156
Posted By nvteja
Reason for low quality of illumina reads

HI All,

Can anyone let me know why is it the case that the read quality is generally lower towards 3' end for solexa ?

Forum: Bioinformatics 01-26-2010, 07:51 AM
Replies: 1
Views: 2,024
Posted By nvteja
Coverage for exon

Hi everyone,

I want to calculate coverage for exon sequences using 454AlignmentInfo.tsv file. I have a bed file of exons. So to calculate coverage is it enough if i average the unqiue depth of...
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