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Forum: Bioinformatics 07-28-2011, 12:13 AM
Replies: 0
Views: 1,667
Posted By mard
has anyone tried variant detection with RNA-seq using GATK?

I'm wondering if anyone has used the GATK tools for variant detection with RNA-seq?

I have some paired end RNA samples that I want to perform variant detection on and am wondering if I can adapt...
Forum: Bioinformatics 06-14-2011, 11:56 PM
Replies: 5
Views: 4,785
Posted By mard
Picard's MergeSamFiles will merge multiple BAM...

Picard's MergeSamFiles will merge multiple BAM files and add all @RGs to the header of the merged BAM.
Forum: Bioinformatics 04-10-2011, 09:18 PM
Replies: 11
Views: 3,526
Posted By mard
Ok, thanks for the info. Where did you get...

Ok, thanks for the info.

Where did you get the fixed vcf file from?
I followed your link above but it brings me to the same 00-All.vcf.gz file I already have (dated Nov 2010):...
Forum: Bioinformatics 04-10-2011, 05:57 PM
Replies: 11
Views: 3,526
Posted By mard
I've just run into this issue now and found your...

I've just run into this issue now and found your post csoong. For SNVs the REF base in my sample's vcf file match what is in the dbSNP132 vcf but the indels seem to be 1 base off (for the ones I've...
Forum: Bioinformatics 12-15-2010, 08:08 PM
Replies: 0
Views: 2,661
Posted By mard
Insert size for Pindel

For indel detection with Pindel insert size needs to be specified for the sam2pindel step.
Is it recommended to use something like Picard's CollectInsertSizeMetrics to determine the mean insert...
Forum: Bioinformatics 11-25-2010, 03:13 PM
Replies: 16
Views: 4,815
Posted By mard
Just to let you know Ensembl class those...

Just to let you know Ensembl class those mutations as "Stop lost".
Forum: Bioinformatics 10-20-2010, 02:17 PM
Replies: 2
Views: 4,091
Posted By mard
Thanks for the suggestion but I ran varFilter...

Thanks for the suggestion but I ran varFilter with a read depth cutoff of 1,000,000 so that can't be the reason. Also I ran varFilter with the -p option aswell which prints the SNPs that are filtered...
Forum: Bioinformatics 10-19-2010, 04:12 PM
Replies: 11
Views: 7,188
Posted By mard
Thanks for the link but I can only see...

Thanks for the link but I can only see explanations for 13 out of the 15 columns there.
This issue has also been reported in this thread:
http://seqanswers.com/forums/showthread.php?t=4234
Forum: Bioinformatics 10-19-2010, 03:12 PM
Replies: 2
Views: 4,091
Posted By mard
MAQ vs BWA/SAMTools - differences in SNP calling algorithm?

I was wondering if anyone has come across this before. Basically we’re getting SNPs that were identified using MAQ, and subsequently validated by Sanger sequencing, not being called by BWA/SAMTools...
Forum: Bioinformatics 09-08-2010, 11:51 PM
Replies: 11
Views: 7,188
Posted By mard
Just wondering if anyone has discovered what the...

Just wondering if anyone has discovered what the extra columns are? I can't find any information on them in the samtools documentation.
Forum: Bioinformatics 07-18-2010, 03:58 PM
Replies: 9
Views: 42,331
Posted By mard
I used the 1000 genomes hg19 reference sequence...

I used the 1000 genomes hg19 reference sequence from:

ftp://ftp.sanger.ac.uk/pub/1000genomes/tk2/main_project_reference/human_g1k_v37.fasta.gz

They already have the haplotype chromosomes...
Forum: Bioinformatics 06-20-2010, 11:39 PM
Replies: 366
Views: 179,811
Posted By mard
That worked. Thanks!

That worked. Thanks!
Forum: Bioinformatics 06-20-2010, 11:20 PM
Replies: 366
Views: 179,811
Posted By mard
Thanks for the quick reply Simon. The...

Thanks for the quick reply Simon.

The command I'm using is:

java -Xmx250m -classpath /Tools/FastQC/ uk.ac.bbsrc.babraham.FastQC.FastQCApplication sequence.fastq

and the sequence.fastq file...
Forum: Bioinformatics 06-20-2010, 05:47 PM
Replies: 366
Views: 179,811
Posted By mard
Hi Simon, Thanks for the new features in...

Hi Simon,

Thanks for the new features in FastQC v0.4.
I just installed v0.4 but got the error below when running it on a fastq file (I had previously run v0.3 on this file with no issues.)
...
Forum: Bioinformatics 05-27-2010, 05:50 PM
Replies: 366
Views: 179,811
Posted By mard
That fixed it. Thanks for that!

That fixed it. Thanks for that!
Forum: Bioinformatics 05-26-2010, 04:21 PM
Replies: 366
Views: 179,811
Posted By mard
I've been using FastQC in interactive mode and...

I've been using FastQC in interactive mode and it's a really great tool.

I just tried to install and run FastQC v0.3 in non-interactive mode but got this error below (I'm running it on a Mac...
Forum: Bioinformatics 03-21-2010, 03:45 PM
Replies: 2
Views: 8,129
Posted By mard
Thanks for the information. I'm pretty new to...

Thanks for the information. I'm pretty new to next-gen analysis so am wondering if it's recommended to remove reads that map to multiple locations before SNP calling?
Forum: Bioinformatics 03-18-2010, 09:40 PM
Replies: 3
Views: 10,547
Posted By mard
Yes it tells you the number of reads that have...

Yes it tells you the number of reads that have been marked as duplicates, as well as the total number of reads. But note that reads that Picard marks as duplicates do not necessarily have identical...
Forum: Bioinformatics 03-16-2010, 04:08 PM
Replies: 2
Views: 8,129
Posted By mard
threshold for duplicate removal?

I was trying out Picard's MarkDuplicates to remove duplicate reads before SNP identification in our targeted resequencing studies but I discovered that Picard classes non-identical reads that map to...
Forum: Bioinformatics 03-09-2010, 09:21 PM
Replies: 24
Views: 19,977
Posted By mard
Thanks for the info. So looks like, for the...

Thanks for the info.

So looks like, for the moment, that the solution is to ignore these warnings in Picard by adding either IGNORE={INVALID_MAPPING_QUALITY,INVALID_CIGAR} (for...
Forum: Bioinformatics 03-09-2010, 05:38 PM
Replies: 24
Views: 19,977
Posted By mard
I am getting a similar error with Picard...

I am getting a similar error with Picard ValidateSamFile.jar after running bwa 0.5.6...


$ java -Xmx4g -jar picard-tools-1.14/ValidateSamFile.jar INPUT=IC201N.sam

[Tue Mar 09 11:35:57 EST...
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