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Forum: Bioinformatics 08-14-2013, 07:42 PM
Replies: 1
Views: 1,022
Posted By jflowers
SAM specification when 1 read from a pair is missing from the SAM

Hello,

After filtering a BAM with paired end reads, there are frequently orphan reads whose mate is no longer in the BAM file itself.

I cannot find any means in which this is tracked in the...
Forum: Bioinformatics 10-26-2012, 01:48 PM
Replies: 4
Views: 2,827
Posted By jflowers
Hi swbarnes2, Here is my output in the...

Hi swbarnes2,

Here is my output in the MarkDuplicates metrics file:

## METRICS CLASS net.sf.picard.sam.DuplicationMetrics
LIBRARY UNPAIRED_READS_EXAMINED READ_PAIRS_EXAMINED ...
Forum: Bioinformatics 10-26-2012, 11:37 AM
Replies: 4
Views: 2,827
Posted By jflowers
Hi vivek, BAM flags won't work for this. ...

Hi vivek,

BAM flags won't work for this. The information about the paired read does not tell you anything about whether the read is still in the file. It only contains information about its...
Forum: Bioinformatics 10-26-2012, 09:48 AM
Replies: 4
Views: 2,827
Posted By jflowers
remove reads from BAM whose mate has already been filtered

Hi,

I have removed duplicates from a paired end run BAM using Picard MarkDuplicates. In some cases, a single read was retained (not exactly sure why, perhaps the retained read was unmapped, but...
Forum: Bioinformatics 10-23-2012, 11:44 AM
Replies: 15
Views: 7,966
Posted By jflowers
Regarding the java.io.FileNotFoundException: (Too...

Regarding the java.io.FileNotFoundException: (Too many open files), there are a number of things to do. Picard sorting seems to open so many files that it can overload default limits on unix...
Forum: Bioinformatics 10-22-2012, 12:37 PM
Replies: 8
Views: 2,631
Posted By jflowers
I think I found the answer to my problem. If you...

I think I found the answer to my problem. If you want breakdancer_max to report reads supporting a variant for each library, you apparently need to use the -a option.
Forum: Bioinformatics 10-22-2012, 12:00 PM
Replies: 8
Views: 2,631
Posted By jflowers
Hi cwhelan, I do want to see how many...

Hi cwhelan,

I do want to see how many supporting reads for each SV call come from each library. However, the output I have generated using bam2cfg.pl followed by breakdancer_max on a merged bam...
Forum: Bioinformatics 10-15-2012, 09:26 AM
Replies: 8
Views: 2,631
Posted By jflowers
I have a related question. I have a merged bam...

I have a related question. I have a merged bam with multiple samples, each from a single library. Can breakdancer be run on the merged bam?
Forum: RNA Sequencing 07-07-2012, 11:23 AM
Replies: 1
Views: 1,834
Posted By jflowers
You don't need to have known indels. The --known...

You don't need to have known indels. The --known argument in the RealignerTargetCreator and IndelRealigner is optional. You should however run both the target creator and realigner for best...
Forum: Bioinformatics 05-18-2012, 09:39 AM
Replies: 3
Views: 2,777
Posted By jflowers
A little late, but I am also running -q option...

A little late, but I am also running -q option and curious if you identified the problem.
Forum: Bioinformatics 05-18-2012, 08:20 AM
Replies: 3
Views: 4,632
Posted By jflowers
Rocketknight, After thinking about it...

Rocketknight,

After thinking about it further, I think your right. Ultimately, it seems like the empirical mismatch rate would be higher for any class of mutations (possibly including the class...
Forum: Bioinformatics 05-17-2012, 01:35 PM
Replies: 3
Views: 4,632
Posted By jflowers
Hi Rocketnight, A little late on the reply,...

Hi Rocketnight,

A little late on the reply, but I'm contemplating some of these issues myself. The mutation bias issue you mentioned seems like it might be a problem only if this class of...
Forum: Bioinformatics 05-17-2012, 12:58 PM
Replies: 15
Views: 10,890
Posted By jflowers
There is a suggested method for non-model...

There is a suggested method for non-model organisms (without a snp db) on the GATK wiki:

http://www.broadinstitute.org/gsa/wiki/index.php/Base_quality_score_recalibration

The proposed method is...
Forum: General 05-15-2012, 10:29 AM
Replies: 0
Views: 1,297
Posted By jflowers
Is GATK Indel Realigner read group aware?

Hello,

I want to realign a multi-sample BAM using the Indel Realigner for eventual SNP-calling. I am following the GATK's "Best Practice Variant Detection with the GATK version 3" which recommends...
Forum: Bioinformatics 03-26-2012, 09:19 AM
Replies: 5
Views: 3,872
Posted By jflowers
That is not necessarily true. If you have...

That is not necessarily true. If you have aligned your data with BWA then the recommended way to get "unique" reads (by Heng Li) is to filter on map quality. See the samtools FAQ under the section...
Forum: Bioinformatics 03-20-2012, 01:12 PM
Replies: 4
Views: 1,951
Posted By jflowers
If you want to stick with samtools, you can use...

If you want to stick with samtools, you can use bcftools and vcfutils.pl vcf2fq (which come with your samtools installation) to get a consensus. This can all be done in one command line, like:
...
Forum: Bioinformatics 03-19-2012, 01:11 PM
Replies: 4
Views: 1,712
Posted By jflowers
volks suggestion works on bam (hence the -b...

volks suggestion works on bam (hence the -b option).
Forum: Bioinformatics 03-19-2012, 01:00 PM
Replies: 20
Views: 3,239
Posted By jflowers
If youre using the latest Ubuntu version (11.10),...

If youre using the latest Ubuntu version (11.10), I just tried quickly installing via the software center and it worked fine. Maybe not the most satisfactory but it should get you up and running.
Forum: Bioinformatics 03-19-2012, 11:51 AM
Replies: 20
Views: 3,239
Posted By jflowers
Are you installing on a unix-based system? (had...

Are you installing on a unix-based system? (had to ask). Which one?
Forum: Bioinformatics 03-16-2012, 02:38 PM
Replies: 1
Views: 4,374
Posted By jflowers
BWA aligned pairs read1=XT:A:U, read2=XT:A:R

Hello,

I've aligned Illumina paired end reads with BWA, filtered using samtools view -f 3 -F 12 ("proper pairs", both mates mapped).

I'm looking at the XT tags and see expected classes, where...
Forum: Bioinformatics 03-13-2012, 12:56 PM
Replies: 11
Views: 3,528
Posted By jflowers
Good, at least now youre not filtering out the...

Good, at least now youre not filtering out the homozygous sites.

If you follow the example carefully from the biostar-exchange link I sent you, you will see that the genotypes (e.g., 0/0,0/1,1/1)...
Forum: Bioinformatics 03-12-2012, 02:35 PM
Replies: 11
Views: 3,528
Posted By jflowers
One final parting shot, given that Heng Li has...

One final parting shot, given that Heng Li has indicated that there is a problem with the genotypes in the vcf (see example at http://biostar.stackexchange.com/que...quality-scores) I would hesitate...
Forum: Bioinformatics 03-12-2012, 02:29 PM
Replies: 11
Views: 3,528
Posted By jflowers
I see the problem. Looking at the source code...

I see the problem. Looking at the source code for vcfutils.pl varFilter there is the following line of code:

next if ($t[4] eq '.'); # skip non-var sites

$t[4] contains data for the fifth...
Forum: Bioinformatics 03-12-2012, 10:03 AM
Replies: 4
Views: 2,278
Posted By jflowers
samtools flagstat or use samtools view -c to the...

samtools flagstat or use samtools view -c to the count the reads
Forum: Bioinformatics 03-12-2012, 08:11 AM
Replies: 13
Views: 4,595
Posted By jflowers
Hi swbarnes2, Just wanted to follow up on...

Hi swbarnes2,

Just wanted to follow up on the issue of generating multiple consensus sequences from mpileup run with multiple BAMs in the event that someone happend upon this thread with the same...
Showing results 1 to 25 of 41

 


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