Question: Error in normalizing lines of sequence in a fasta file using NormalizeFasta (Picard)
gravatar for Raheleh
12 months ago by
Raheleh110 wrote:

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!

ADD COMMENTlink modified 12 months ago • written 12 months ago by Raheleh110
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