Question

Alignment Viewer

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3.1 years ago

bandanaschapagain ▴ 30

Hi, I have mitochondrial DNA sequences bam files which are the output of the alignment to its references. I used bcftools to identify the variants. I am now advised to confirm about the variants manually. I am looking forward to know about the current methods to verify the identified variants in the vcf files. I highly appreciated any suggestions at this point.

sequencing alignment • 1.1k views

ADD COMMENT • link updated 3.1 years ago by GenoMax 141k • written 3.1 years ago by bandanaschapagain ▴ 30

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Experimental verification is still done using sanger sequencing.

ADD REPLY • link 3.1 years ago by GenoMax 141k

score 1 · Answer 1 · 2021-03-28

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3.1 years ago

rodolfo.peacewalker ▴ 390

Hi!

I suggest you to use IGV in order to take a look at your files for variant identification or visualization.

ADD COMMENT • link 3.1 years ago by rodolfo.peacewalker ▴ 390

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Is there any suitable tutorial for using IGV through commmand line?

ADD REPLY • link 3.1 years ago by bandanaschapagain ▴ 30

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IGV is predominantly a viewer meant to be used interactively using the graphical interface. IGV includes a command line utility called igvtools (LINK).

ADD REPLY • link 3.1 years ago by GenoMax 141k