Convert SAM to an aligned multi-fasta

SEQanswers June Challenge Has Begun!

The competition has begun! We're giving away a $50 Amazon gift card to the member who answers the most questions on our site during the month. We want to encourage our community members to share their knowledge and help each other out by answering questions related to sequencing technologies, genomics, and bioinformatics. The competition is open to all members of the site, and the winner will be announced at the beginning of July. Best of luck!

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Jon17

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Join Date: Jun 2016

Posts: 15
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#16

09-18-2017, 12:12 PM

I figured it out:

java -jar /data1/jvarkit/dist/sam4weblogo.jar -r H19WT:1-174 SAMPLE_274_R1_val_1_bismark_bt2_pe-novosorted.bam

H19WT = chromosome / amplicon / reference name
1-174 = full length of amplicon
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