qiaseq panel fastq to vcf

0

Entering edit mode

3.8 years ago

tadeja.klade ▴ 10

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.

ngs qiaseq freebayes • 1.1k views

ADD COMMENT • link 3.8 years ago by tadeja.klade ▴ 10

1

Entering edit mode

Hello, you could try running this qiaseq-dna workflow

ADD REPLY • link 3.8 years ago by desouzareis.r ▴ 280

0

Entering edit mode

Thank you very much, I will try

ADD REPLY • link 3.8 years ago by tadeja.klade ▴ 10

0

Entering edit mode

Sorry but I get an error. ImportError: No module named qiaseq-smcounter-v1.sm_counter Can you help me with it, please?

ADD REPLY • link 3.8 years ago by tadeja.klade ▴ 10

0

Entering edit mode

Hi, looks like the submodule repository was removed. However I was able to find another repo with the modeule here.