Question: (Closed) BAM to VCF format
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gravatar for nvlinh.dth
22 months ago by
nvlinh.dth10
nvlinh.dth10 wrote:

I'm analyzing NGS data on website:usegalaxy.org in the following steps: 1. Fastq file Raw reads QC FASTQ Groomer FASTQ Trimmer

Convert to Fastqsanger file

Map to reference (Map with BWA for Illumina)

Convert SAM file to BAM

Mark to Duplicates (Picard tools) or make a VCF file.

Analysis by GATK tools such as: Indel realignment, Base Recalibration, Variant Calling, variant Filtering, annotation (SnpEff)

I have a problem at step 5 , I don't know how to do. Would you like help me, please.

galaxy • 2.3k views
ADD COMMENTlink written 22 months ago by nvlinh.dth10

Hello nvlinh.dth!

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Cheers!

ADD REPLYlink written 22 months ago by Jennifer Hillman Jackson23k
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