User: micro32uvas

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Posts by micro32uvas

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Comment: C: RealignerTargetCreator inputs multiple Bams??
... i cannot understand how would this omit realignment. wouldn't realigner give further improvement in terms of mapping and enhanced calibration. If you could precisely share the command that would cover all of it, it would be highly appreciated ...
written 4 days ago by micro32uvas0
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Comment: C: RealignerTargetCreator inputs multiple Bams??
... Can you kindly elaborate this Devon? Actually i am working on Haplotypecaller but along with this preprocessing phase. i.e. after marking duplicates, now i am up with realign target creator, indel realigner and then base calibration. Then would be the haplotype calling using haplotype caller. Your ...
written 4 days ago by micro32uvas0
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Comment: C: RealignerTargetCreator inputs multiple Bams??
... You just solved my problem Pearl :) I'll get back here, if there's still some errors ...
written 4 days ago by micro32uvas0
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Comment: C: RealignerTargetCreator inputs multiple Bams??
... I never prefer Galaxy anyways, and yes its very limited as well. Its just I was missing the -I switch everytime, which was creating the problem. I just checked in galaxy for the given options there, if i was missing any. Thanks Devon ...
written 4 days ago by micro32uvas0
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RealignerTargetCreator inputs multiple Bams??
... Hello Everyone, I have been working with RealignerTargetCreator and in its pages, [RealignerTargetCreator][1]. It states that it takes multiple inputs as Bam. But its not taking it. when I checked Galaxy.it stated that GenomeAnalysisTK: RealignerTargetCreator accepts **an** aligned BAM input file. ...
gatk bam realignertargetcreator written 4 days ago by micro32uvas0 • updated 4 days ago by Devon Ryan65k
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Comment: C: Is my file created completely
... **bwa mem -t 48 genome.fa reads.fastq | samtools sort -@ 20 -O BAM -o output.bam -** It didnt work, following are the errors: sort: invalid option -- 'O' open: No such file or directory [bam_sort_core] fail to open file BAM [M::bwa_idx_load_from_disk] read 0 ALT contigs ...
written 12 days ago by micro32uvas0
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Comment: C: Is my file created completely
... No viewing? no samtools view command? In that case we are not indexing either. Additionally the bam created here, would be sorted right? ...
written 12 days ago by micro32uvas0
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Comment: C: Is my file created completely
... Here's what I have been working on: But somehow this isnt working well on bam filling #!/bin/bash bwa mem -t 48 -M ref.fa data_1.fastq data_2.fastq >mini-data.sam samtools view -b -S -F 2308 -t 48 data.sam >data_unsorted.bam samtools sort data_unsorted.bam data| samtools index ...
written 12 days ago by micro32uvas0 • updated 12 days ago by WouterDeCoster17k
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Comment: C: Is my file created completely
... Hi Wouter, Could you guide me to the command for Bam file creation directly, instead of sam file. I wantedto do it directly in a single command with pipelines but it wont work that way. ...
written 12 days ago by micro32uvas0
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Comment: C: Is my file created completely
... Its driving me crazy, but yes worst case scenerios are always there at the door step just exactly when you set to go all smooth. Biostars is a great blessing though! ...
written 14 days ago by micro32uvas0

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