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Old 01-18-2012, 05:32 PM   #1
aperdomos
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Default How to analyse and visualize “vcrf” files (*vcrfpileup; *pileup*) with samtools-other

Hello everyone,

I got some files with DNA sequencing preliminary data from a partner lab. Before they sent me these data, they were processed using variant calling with the samtools pileup option (I don’t have access to the raw data); therefore, these files are in *vcrfpileup* and *pileup* formats. I noticed that these files are listing only the positions that can be determined as different from reference in a consistent manner. However, I still need to distinguish regions without variants due to their homology to reference from regions not having variants because they were not covered at all.

On the other topic, but same matter, In an attempt to access, visualize and obtain the information about specific DNA regions to design some set primers, I have been trying to access and visualize the alignment of these files using samtools tview and bcftools view. However, the former require that the file be in BAM-SAM format (errors: [ban_header_read] EOF marker is absent; main_samview] fail to Read the header. The latter show me the error ([bcf_sync] incorrect number of fields (0= !5) at 0:0.)

Does anyone know what can I do to distinguish regions without variants due to their homology to reference from regions not having variants using the file formats: aps.vcrfpileup and aps.pileup?

Does anyone know a better way to visualize the alignments between the reference genome and NGS data using files that are in format *vcrfpileu* and *pileup*?

Many thanks,

Alvaro
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Old 01-18-2012, 10:12 PM   #2
swbarnes2
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The pileup has one line per base of your sequence, but if a base is totally uncovered by reads, it should be missing. So you could parse that to find regions with no coverage. Yeah, the vcf won't help you there.

And yeah, tview won't take a pileup, but you can eyeball a pileup with any text editor. tview, or IGV, take bams as input, which you don't have. Whoever made the pileups and vcfs used a bam to make them, so the easiest thing is to ask for that.
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Old 01-19-2012, 12:25 AM   #3
aperdomos
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Swbarnes2.

Many thanks for your answer; it helped me to clarify some of my concerns. I was using the text editor to explore the files (pileups); however, the big number of samples from different individuals and the size of the genome region studied pushed me to ask for possible solutions to using these files. I will ask for the BAM file, I hope I can access them.
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