qiaseq panel fastq to vcf
Hello to every one, I have QIAseq Targeted DNA Panel and when I read about it I can see: Digital DNA sequencing is a unique approach to detect low-frequency variants with high confidence by overcoming the issues of PCR duplicates, false positives and library bias. Does it mean that I do not need to go through all the common steps to analyze the data? Of course, I have fastq files and I need vcf files. Which steps should I do? (trimming, alignment, marking PCR duplicates obviously not or?).
Until now I have used GATK-Haplotypecaller, is it better to use freebayes?
Thank you for all your recommendations.
• 1,877 views
•
link
written
by
tadeja.klade •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Removing duplicates
written by quentinperriere •
-
PCR duplicates in FFPE RNASeq
written by Gama313
-
NuGEN Ovation RRBS Methyl-Seq System - How to use nudup.py to remove PCR duplicates- RRBS
written by BB •
-
Viral Amplicon Haplotype Calling
written by geneticatt •
-
read group, fastq files, and multiple run ids
written by Cricket •
-
Variant discrepancy between technical replicates
written by kspata
-
How do Read Alignment tools detect PCR duplicates?
written by madischapel •
-
If we use MACS2 do we need to remove duplicate sequences with samtools rmdup ?
written by salamandra
-
NGS preprocessing pipleine for ion torrent data
written by Noushin N
-
Rare Allele Quantification
written by thedusseldorfer •
Hello, you could try running this qiaseq-dna workflow
Thank you very much, I will try
Sorry but I get an error. ImportError: No module named qiaseq-smcounter-v1.sm_counter Can you help me with it, please?
Hi, looks like the submodule repository was removed. However I was able to find another repo with the modeule here.
Hi, it works. Thank you very much, have a nice day.