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

I'm analyzing NGS data on 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 • 3.5k views
ADD COMMENTlink written 2.7 years ago by nvlinh.dth10

Hello nvlinh.dth!

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ADD REPLYlink written 2.7 years ago by Jennifer Hillman Jackson25k
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