Question: Error in normalizing lines of sequence in a fasta file using NormalizeFasta (Picard)
0
gravatar for Raheleh
12 months ago by
Raheleh110
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
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1996 users visited in the last hour