It is possibly being thrown off by termination blocks on each of the
non-final chunks. I tried the same using rtg bgzip --no-terminate when
compressing each of the chunks (you could leave the termination block on
the final one) and rtg index to perform the indexing, and then tabix was
able to perform the extractions just fine.
Cheers,
Len.
On 13 May 2015 at 23:17, Kanterakis, Efstathios <ekantera...@illumina.com>
wrote:
> Hello,
> The following routine seems to produce invalid tabix indices (samtools
> 1.2):
> zgrep '^chr1' some.vcf.gz > chr1.vcf
> zgrep '^chr2' some.vcf.gz > chr2.vcf
> zgrep '^#' some.vcf.gz > header.vcf
> cat header.vcf chr1.vcf > chr1_h.vcf
> bgzip chr1_h.vcf
> bgzip chr2.vcf
> cat chr1_h.vcf.gz chr2.vcf.gz > test.vcf.gz
> tabix test.vcf.gz
> tabix test.vcf.gz chr2 # blank
> tabix test.vcf.gz chr1 # works
>
> bgzip -d test.vcf.gz
> bgzip test.vcf
> tabix test.vcf.gz
> tabix test.vcf.gz chr2 # works now
>
> I was under the impression that bgzipped files are directly cat'able. Is
> this a bug?
>
> Thank you,
> Stathis
>
>
> -----Original Message-----
> From: Christian Ruckert [mailto:cruck...@uni-muenster.de]
> Sent: 13 May 2015 10:19
> To: samtools-help@lists.sourceforge.net
> Subject: [Samtools-help] mpileup: tradeoff between runtime and accuracy
>
> So far I called variants on my high coverage targeted sequencing data with
> the following mpileup settings:
>
> samtools mpileup -ug -Q 5 -d 2000 -L 2000 -f hg19.fasta -l target.bed
> in.bam | ...
>
> bam files are around 300 megabytes, target.bed contains 10 genes and
> runtime was pretty acceptable with around 1-2 hours. But this setting has
> two major drawbacks:
>
> - I missed indels with a coverage higher than 2000 because of the -L
> paramter
> - Even if I think SNPs are called correctly with this -d value the DP and
> DP4 values are higher than 2000 (which I don't understand
> completely) but don't contain all reads as shown in IGV
>
> So I tried the following settings
>
> samtools mpileup -ug -Q 0 -d 1000000 -L 1000000 -f hg19.fasta -l
> target.bed in.bam | ...
>
> Now "nothing" is missed and DP values are correct but the program runs for
> more than 12 hours, which I think is to long given my relatively small
> input data.
>
> I already tried the --no-BAQ parameter with little success. So my
> questions:
>
> Is my runtime comparable to others, which parameters have the most
> influence on runtime and how can I get correct DP values even if not using
> all reads for variant calling?
>
> Best,
> Christian
>
>
> ------------------------------------------------------------------------------
> One dashboard for servers and applications across Physical-Virtual-Cloud
> Widest out-of-the-box monitoring support with 50+ applications Performance
> metrics, stats and reports that give you Actionable Insights Deep dive
> visibility with transaction tracing using APM Insight.
> http://ad.doubleclick.net/ddm/clk/290420510;117567292;y
> _______________________________________________
> Samtools-help mailing list
> Samtools-help@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/samtools-help
>
>
> ------------------------------------------------------------------------------
> One dashboard for servers and applications across Physical-Virtual-Cloud
> Widest out-of-the-box monitoring support with 50+ applications
> Performance metrics, stats and reports that give you Actionable Insights
> Deep dive visibility with transaction tracing using APM Insight.
> http://ad.doubleclick.net/ddm/clk/290420510;117567292;y
> _______________________________________________
> Samtools-help mailing list
> Samtools-help@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/samtools-help
>
--
Len Trigg, PhD
Director of Research and Development
Real Time Genomics
www.realtimegenomics.com
------------------------------------------------------------------------------
One dashboard for servers and applications across Physical-Virtual-Cloud
Widest out-of-the-box monitoring support with 50+ applications
Performance metrics, stats and reports that give you Actionable Insights
Deep dive visibility with transaction tracing using APM Insight.
http://ad.doubleclick.net/ddm/clk/290420510;117567292;y
_______________________________________________
Samtools-help mailing list
Samtools-help@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/samtools-help
