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Forum: Bioinformatics 12-22-2011, 05:14 AM
Replies: 4
Views: 3,070
Posted By alma
Unhappy Problem with samtools/bcftools


I am trying to call SNPs and indels from some bam files and I tried the following commands as given in the samtools/bcftools manual:

samtools mpileup -uf reference.fa aln1.bam | bcftools...
Forum: Bioinformatics 07-07-2011, 02:46 AM
Replies: 0
Views: 2,026
Posted By alma
Question Interpreting Local Realignment results from GATK

Hi there. I need some help in interpreting the result of Local Realignment (around indels) using GATK please. I am new to using the package and trying to understand it. I have run the local...
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