Error in normalizing lines of sequence in a fasta file using NormalizeFasta (Picard)
0
0
Entering edit mode
5.4 years ago
Raheleh ▴ 260

Hi, I want to run VarScan fpfilter for 3 .hc.vcf files (somatic, germline, LOH), however when I run this command

bam-readcount -q 1 -b 20 -l all.Somatic.hc.var -f hg38.fa tumor.bam > all.Somatic.hc.readcount

I get this error

[fai_load] build FASTA index. [fail_load_core] different line length in sequence ‘(null)’

Based on google search I found that I have to use Picard to normalize lines of sequence. But when I run this command java -jar picard.jar NormalizeFasta -I hg38.fasta -O normalized_hg38.fasta I get this error “

Invalid argument ‘-I’

I also run with -i and without argument but still get the same error

Invalid argument

I stuck in this step :( can anyone help me with this errors? Thanks!

picard NormalizeFasta varscan bam-readcount • 1.3k views
ADD COMMENT

Login before adding your answer.

Traffic: 2408 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6