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Search: Posts Made By: wangzkai
Forum: Bioinformatics 06-27-2016, 05:19 PM
Replies: 0
Views: 1,528
Posted By wangzkai
Strand bias in variant calls

Most, if not all, strand bias filters of SNV calls require that a variant to be observed on reads aligned to both directions. While I understand the rationale behind this is to avoid strand specific...
Forum: Bioinformatics 10-24-2011, 03:25 PM
Replies: 1
Views: 3,380
Posted By wangzkai
Question on the speed of bwa aln

Hi,

I am trying to use bwa to align ~800 million 100bp PE reads from a whole genome dataset generated on the Illumina platform. These are "anomaly" reads which are either unmapped reads, or...
Forum: Bioinformatics 05-15-2010, 12:38 AM
Replies: 5
Views: 6,539
Posted By wangzkai
Question SNP quality score in Samtools pileup

Hi,

I was examining the pileup by Samtools at a particular base of interest:
...
Forum: Bioinformatics 05-06-2010, 07:28 PM
Replies: 3
Views: 3,082
Posted By wangzkai
Sorted bam

I have a bam file which were already sorted (by coordinates) using "samtools sort". However, when I tried to remove duplicate reads using picard's "MarkDuplicates" function, it failed saying that the...
Forum: Bioinformatics 05-01-2010, 01:31 PM
Replies: 1
Views: 2,163
Posted By wangzkai
Samtools merge

A quick question on Samtools merge:

Will the output bam file from Samtools merge remain to be sorted by chromosome coordinate?

Thanks!
Forum: Bioinformatics 04-24-2010, 09:56 PM
Replies: 2
Views: 7,124
Posted By wangzkai
Picard MarkDuplicates

This may be a naive question, but I was trying to figure out whether I should set "REMOVE_DUPLICATES" to true or false when using picard's "MarkDuplicates" to remove duplicate reads. Since I want to...
Forum: Bioinformatics 03-31-2010, 10:11 PM
Replies: 3
Views: 4,626
Posted By wangzkai
Thank you, nilshomer. On the samtools manual...

Thank you, nilshomer. On the samtools manual page, there are two rmdup commands:

samtools rmdup <input.srt.bam> <out.bam>

and

samtools rmdupse <input.srt.bam> <out.bam>

So does this mean...
Forum: Bioinformatics 03-31-2010, 08:58 PM
Replies: 3
Views: 4,626
Posted By wangzkai
Question A question on samtools rmdup

Hi,

I was studying the SAM protocol on SourceForge:

http://sourceforge.net/apps/mediawiki/samtools/index.php?title=SAM_protocol

There is one command that merge sorted alignments and remove...
Forum: Events / Conferences 03-13-2010, 08:23 PM
Replies: 8
Views: 3,563
Posted By wangzkai
That is fine. I am not a postdoc. But I remain...

That is fine. I am not a postdoc. But I remain interested in the free pass. Please let me know if I can have it.
Forum: Events / Conferences 03-13-2010, 01:08 PM
Replies: 8
Views: 3,563
Posted By wangzkai
By the way, what do you mean by "a free pass"?...

By the way, what do you mean by "a free pass"? Have you already registered at the conference and would like to give your registration to someone else? Just want to clarify ...
Forum: Events / Conferences 03-13-2010, 01:05 PM
Replies: 8
Views: 3,563
Posted By wangzkai
I am interested in attending the conference. I am...

I am interested in attending the conference. I am in San Diego so if I get the pass I will be sure to commit 100%.
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