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Search: Posts Made By: MGCBrown
Forum: Bioinformatics 09-19-2017, 05:41 AM
Replies: 15
Views: 8,518
Posted By MGCBrown
Does anyone have the SNP_in_ORF_nonsyn.pl script...

Does anyone have the SNP_in_ORF_nonsyn.pl script that was described in this thread? The link to the script is no longer in use (http://users.ugent.be/~slvbelle/NGS/)

Any info would be great!
Forum: Bioinformatics 07-05-2017, 06:06 AM
Replies: 1
Views: 796
Posted By MGCBrown
How to extract SNPs between samples, but not between samples and reference.

Hello,

I have used samtools mpileup, and bcftools call/filter (v1.5) to call SNPs between 4 samples and a de novo reference transcriptome.

I'm interested in extracting SNPs that occur between...
Forum: Bioinformatics 06-28-2017, 11:00 AM
Replies: 3
Views: 778
Posted By MGCBrown
Thanks for the reply, I appreciate it. I'm using...

Thanks for the reply, I appreciate it. I'm using samtools and bcftools -1.4.1. I'll try running it now. Thanks again.
Forum: Bioinformatics 06-28-2017, 05:29 AM
Replies: 3
Views: 778
Posted By MGCBrown
Angry Very strange .vcf output after running samtools and bcftools

Hello,

After I run the samtools variant calling pipeline, I'm not getting the conventional .vcf output that I was expecting. Any advice or insight would be greatly appreciated.

Here is my...
Forum: Bioinformatics 06-22-2017, 10:38 AM
Replies: 2
Views: 665
Posted By MGCBrown
Thank you, Devon!

Thank you, Devon!
Forum: RNA Sequencing 06-22-2017, 08:14 AM
Replies: 0
Views: 862
Posted By MGCBrown
Question Confused about how to approach SNP discovery in hybridizing sister species

Hello,

I'm new to genomics, but I have assembled a de novo transcriptome (Trinity), and have alignments for two sister species (two individuals per species = 4 individuals total) - the same...
Forum: Bioinformatics 06-21-2017, 09:58 AM
Replies: 2
Views: 665
Posted By MGCBrown
Is indexing .bam files before samtools mpileup necessary?

Is indexing your .bam files a necessary step for running the samtools variant calling pipeline (ie samtools mpileup, bcftools view etc)?

I know that indexing your genome/transcriptome is a...
Forum: Bioinformatics 06-20-2017, 10:27 AM
Replies: 1
Views: 542
Posted By MGCBrown
Issues with samtools mpileup and bcftools view

Hello,

I've been having some trouble interpreting the outputs from samtools variant calling pipeline. I'm working with a de novo transcriptome assembly and a .bam file containing the reads from 1...
Forum: Bioinformatics 06-15-2017, 05:55 AM
Replies: 3
Views: 807
Posted By MGCBrown
Thanks for the help! I see that when I open my...

Thanks for the help! I see that when I open my ssh client on a different computer, the files are no longer using the VCard extension.

Thanks again.
Forum: Bioinformatics 06-14-2017, 10:32 AM
Replies: 3
Views: 807
Posted By MGCBrown
Question samtools SNP calling pipeline outputs VCard file instead of variant call format (VCF)

Hello,

I used this workflow to call SNPs on bam files that were aligned to a reference de novo transcriptome assembly:

samtools mpileup -uf normalized_Trinity.fasta aln2.bam aln2.bam |...
Forum: Bioinformatics 05-25-2017, 12:39 PM
Replies: 3
Views: 732
Posted By MGCBrown
Thanks for the tips! I've opened the .vcf...

Thanks for the tips!

I've opened the .vcf file in Notepad++. I've copied two components of my .vcf file below as one of the components looks OK but the other, not so much. Do you think someone...
Forum: Bioinformatics 05-25-2017, 11:48 AM
Replies: 3
Views: 732
Posted By MGCBrown
It seems that a more pressing issue is that the...

It seems that a more pressing issue is that the SAMtools variant calling pipeline has created vCalendar files and not VCF (variant call format) files.

I followed this pipeline:
samtools mpileup...
Forum: Bioinformatics 05-25-2017, 11:18 AM
Replies: 1
Views: 497
Posted By MGCBrown
I've noticed that what I thought was a .vcf file...

I've noticed that what I thought was a .vcf file created with the SAMtools variant calling pipeline is actually a vCalendar file.

Any explanations as to why I have a vCalendar file? I'm guessing...
Forum: Bioinformatics 05-25-2017, 10:46 AM
Replies: 1
Views: 497
Posted By MGCBrown
undescribed snpEff error after command execution

Hello,

I'm trying to use snpEff to annotate variants in a .vcf file that I called with SAMtools.

Here is my command:

java -Xmx4g -jar snpEff.jar -v spetri2.86 glaucomysvarfiltered.vcf >...
Forum: Bioinformatics 05-25-2017, 09:34 AM
Replies: 3
Views: 732
Posted By MGCBrown
Question ANNOVAR to annotate variants called with the SAMtools pipeline

Hello,

I'm new to this forum and bioinformatics for that matter.

I'm studying functional genomics and ecology of hybridization in flying squirrels, with the goal of identifying SNPs between...
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