Entering edit mode
5.9 years ago
shuksi1984
▴
60
I ran following command:
java -Xmx4g -jar /path/to/gatk3.8.jar -T RealignerTargetCreator -R /path/to/Homo_sapiens_assembly38.fasta -I SP1_markduplicate.bam -o SP1_realignedtargets.list
I got following error message:
ERROR MESSAGE: Bad input: We encountered a non-standard non-IUPAC base in the provided reference: '92'
What does this mean? Did Homo_sapiens_assembly38.fasta got corrupted?
GATK3.8
Output of
is:
what devon said:
futhermore there is a 'O'.
I also suggest you have a look at this fasta file:
Can you share the link to download hg38gatkbundle reference genome? I am trying with the given link:
ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/hg38/Homo_sapiens_assembly38.fasta.gz
there is no problem with that resource. your data is corrupted.
bam file is corrupted?
try to understand what I've done in my previous comment please C: GATK3 error message
I ran the above command and got same output. I could not find any file in my working directory, except the output as shown above. I am unable to understand. Kindly, explain