After aligning paired-end 100bp reads to a reference genome, I am getting very low properly paired percentage:
369208441 0 total (QC-passed...
9 results in 0.0021 seconds.
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bwa mem - low properly paired percentage
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GATK multisample vcf to BayeScan input
Hi all,
I am trying to convert a "multi-sample (population)" vcf file from GATK obtained using a "joint genotyping workflow"... -
Generate a SAM file containing aligned reads GATK Error
Hello All,
I am a new bee here and entirely new to bioinformatics, I am working on the tutorial of GATK. I using its command to map and mark duplicates... -
Need of read group information for paired end library
I have a single BAM file created while merging fastq files for both R1 and R2 for a single cell RNAseq. Now I just want to run GATK to see if some variants... -
GATK RNA-Seq pathway Split 'n' Trim- problems with .bai and .fai index compatibility
I am processing aligned RNA-Seq data to get phased haplotypes of novel genes in sea stars. I am working through the analysis pipeline that used the Genome...Last edited by gwilymh; 11-17-2014, 06:03 PM. Reason: Specifying the specific part of the pipeline where I had the problem -
Gatk vqsr
What does VQSR actually do? It improves the score? It filters the variants? or exactly what?
Is it an alternative for VariantFiltering based on... -
Looking for GATK manual - site down
Hi everyone,
The GATK web site is down for a few days. Has anyone got GATK mauals in pdf or similar formats? I'm just looking for some... -
Which GATK step should be multisample?
Hi everybody,
I am new in NGS analysis and hope not to ask something already solved (or discussed), in that case please only refer me to the right... -
Performance bottlenecks in sequence analysis pipelines
Hi,
Has anyone who has used the GATK pipeline and/or sequence alignment tools such as BWA and stampy have a feel for what the worst bottlenecks...
