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Posts by le.marcorin
... Hi! I'm trying to get the allele count for some snps in my bam files. The variant calling was done by haplotypeCaller. The allele count in the output doesn't represent the real number of reads I have in my bam file, whitch is what I want. I tried with bcftools mpileup, but the output only shows ge ...
Comment: C: Variant Function Prediction
... I am using Haploreg to study some non-coding regions but I 'm having problems understanding those values in the 'Regulatory motifs altered' area in the end of the page. Could you help me? I already read the paper from Kheradpour and Kellis, 2013, but it didn't help ...
... Hi! I'm working with Illumina Miseq reads and i'm having some trouble with variant calling. I used cutadapt for trimming adapters, bwa for alignment and GATK HaplotypeCaller (-dontUseSoftClippedBases) for variant calling. I also used vcfx (http://www.castelli-lab.net/apps/apps_vcfx.php) to better c ...
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