How to remove INDELS/SNPs from a bed file
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Cian • 0
@831b6808
Last seen 7 days ago
Ireland

I am trying to remove INDELS from a .bed file because I only need the SNP data. My data is set up so column 1 = chromosome, 2 = start position, 3 = stop position, 4-5 = reference-alternative nucleotide and 6 = patient ID. how do I remove the INDELS along with rest of that row from the file?

Code should be placed in three backticks as shown below


# include your problematic code here with any corresponding output 
# please also include the results of running the following in an R session 

sessionInfo( )
SNP • 60 views
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@james-w-macdonald-5106
Last seen 19 minutes ago
United States

That isn't a bed file, by definition. It's more of a free-form file with genomic positions. But still easy enough to deal with. Here's a self-contained example, where I am assuming that your 'bed' file follows the normal convention for a bed file and is 0-based, half open. In Bioconductor we use 1-based, fully closed numbering. If you don't know what that means, read this.

## Fake-o data
## You would have to read your data in using read.table
> starts <-  seq(234, 237, 1)
> d.f <- data.frame(chr = rep("chr1", 4), start = starts, end = starts +c(1,5,1,1), ref = c("A","T","C","G"), alt = c("C", "ACGTG","A","T"), user = 1:4)
> d.f
   chr start end ref   alt user
1 chr1   234 235   A     C    1
2 chr1   235 240   T ACGTG    2
3 chr1   236 237   C     A    3
4 chr1   237 238   G     T    4

## Note we add 1 to the start position to convert to 1-based, fully closed
> gr <- GRanges(d.f[,1], IRanges(d.f[,2] + 1L, d.f[,3]), ref = d.f[,4], alt = d.f[,5], id = d.f[,6])
> gr
GRanges object with 4 ranges and 3 metadata columns:
      seqnames    ranges strand |         ref         alt        id
         <Rle> <IRanges>  <Rle> | <character> <character> <integer>
  [1]     chr1       235      * |           A           C         1
  [2]     chr1   236-240      * |           T       ACGTG         2
  [3]     chr1       237      * |           C           A         3
  [4]     chr1       238      * |           G           T         4
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths
> width(gr)
[1] 1 5 1 1
> newgr <- gr[width(gr) == 1L]
> newgr
GRanges object with 3 ranges and 3 metadata columns:
      seqnames    ranges strand |         ref         alt        id
         <Rle> <IRanges>  <Rle> | <character> <character> <integer>
  [1]     chr1       235      * |           A           C         1
  [2]     chr1       237      * |           C           A         3
  [3]     chr1       238      * |           G           T         4
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths

> as(newgr, "data.frame")
  seqnames start end width strand ref alt id
1     chr1   235 235     1      *   A   C  1
2     chr1   237 237     1      *   C   A  3
3     chr1   238 238     1      *   G   T  4

I trust you know how to write that resulting data.frame to disk.

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