User: evelyn
evelyn • 130
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Posts by evelyn
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Comment:
C: freebayes error variant calling
... I have changed the `SM` but I am not sure how to change `ID` which `freebayes` is complaining about. ...
written 6 months ago by
evelyn • 130
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Comment:
C: freebayes error variant calling
... I have checked the fastq file header:
@S79.1 1 length=150
CAAAAGATTATTTTAGAAAGCACAATGTGAGGACAGAACTCTACAAAGTGCTGAATGCAAAGAAATACAATTCTGCAGATCCAATTCCATTAAGATTTAAGTGATGCCCCTACTTTTCCAAGGTCCTCAAGTTCCTTTGAGATTTGCTCC
+S79.1 1 length=150
A<, ...
written 6 months ago by
evelyn • 130
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Comment:
C: freebayes error variant calling
... Thank you! I got the fastq files from a collaborator. I don't have information about these variables. What can be the best way to find this information? ...
written 6 months ago by
evelyn • 130
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Comment:
C: freebayes error variant calling
... I understand I need to add read groups information. But I could not find where to look for this information. How to check what is RGID, RGLB, RGPL, RGPU for my samples in order to add this information using picard. ...
written 6 months ago by
evelyn • 130
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Comment:
C: freebayes error variant calling
... It shows nothing for read group. ...
written 6 months ago by
evelyn • 130
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Comment:
C: freebayes error variant calling
... Thank you! How can I add the readgroup information to bam files using picard. Where can I find the readgroup information for the data I have. ...
written 6 months ago by
evelyn • 130
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Comment:
C: freebayes error variant calling
... I checked the readgroups for the two samples it is showing error for using:
samtools view -H sample.bam | grep "SM:"
It is showing different names for both the files based on their respective sample names. ...
written 6 months ago by
evelyn • 130
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... Hello,
I am using `freebayes` for variant calling using:
list=list.txt
freebayes -f transcripts.fasta -L $list
--ploidy 2 \
--min-alternate-fraction 0.2 \
--min-alternate-count 2 \
--min-coverage 3 ...
written 6 months ago by
evelyn • 130
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... It shows, `@RG ID:4 LB:lib1 PL:ILLUMINA SM:20 PU:unit1` ...
written 6 months ago by
evelyn • 130
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... Hello,
I am using following command to create a `vcf` file with `freebayes`:
freebayes -f transcripts.fasta duplicates.bam --max-complex-gap 1 \
--theta 0.01 \
--ploidy 2 \
--min-alternate-fraction 0.2 \
...
written 6 months ago by
evelyn • 130
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