Question: Converting tsv into bam file
gravatar for vinayjrao
2 days ago by
inStem, India
vinayjrao180 wrote:


We have obtained data from the European Genome-Phenome Archive, and the said data has been provided in .tsv format. In the summary of the dataset, they claim that this is a sequence file, so I am assuming that these could be indexed bam files. I would like to know whether there is a way to convert it to bam, so that I can go ahead and identify variants from the same?

Below is a sample of the file

locus ploidy chromosome begin end zygosity varType reference allele1Seq allele2Seq allele1VarScoreVAF allele2VarScoreVAF allele1VarScoreEAF allele2VarScoreEAF allele1VarQuality allele2VarQuality allele1HapLink allele2HapLink allele1XRef allele2XRef evidenceIntervalId allele1ReadCount allele2ReadCount referenceAlleleReadCount totalReadCount allele1Gene allele2Gene pfam miRBaseId repeatMasker segDupOverlap relativeCoverageDiploid calledPloidy relativeCoverageNondiploid calledLevel

1 2 chr1 0 7000 no-call no-ref = ? ?

2 2 chr1 7000 9083 no-call complex = ? ?

                             1.23 N 1.12 1.003

3 2 chr1 9083 11050 hom ref = = =

                              1.23 N 1.12 1.003

Please note that each space indicates a single column. Also, the second lines of the second and third sections are indented towards the right.

Thanks in advance

linux sequencing R genome • 58 views
ADD COMMENTlink modified 2 days ago by swbarnes29.1k • written 2 days ago by vinayjrao180

Please use the formatting bar (especially the code option) to present your post better. It is difficult to discern information in your post above at this time.

Thank you!

ADD REPLYlink written 2 days ago by genomax92k
gravatar for swbarnes2
2 days ago by
United States
swbarnes29.1k wrote:

What you posted is not in any way, shape, or form what a bam file should look like. It looks like it has variants already, since it says "hom ref"

ADD COMMENTlink written 2 days ago by swbarnes29.1k

I notice that, so what kind of file might this be? Should I try converting to vcf for annotation?

ADD REPLYlink written 2 days ago by vinayjrao180
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