Question

PLINK --allow-extra-chr error

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4.2 years ago

dumeir ▴ 20

Hi,

I've got .bed/.bim/.fam SNP files and am using physical bp positions to extract SNP subsets in PLINK (version 1.9). I got my coordinates from UCSC Table Browser so some of the chromosome IDs are unusual, like "6_ssto_hap7" or "Un_gl000211".

I tried using --allow-extra-chr 0 to include these but it doesn't seem to be working as I still get the same error

Error: Invalid chromosome code on line 938486 of --extract range file.

(Line 938486 is where the unusual chromosome IDs start)

I've been using this command:

plink --bfile <filename> --extract range <coordinates.txt> --make-bed --out <newfile> --allow-extra-chr 0

If I delete all the coordinates with the unusual chromsome IDs, I can successfully extract SNPs.

Any suggestions to fix this?

Thanks!

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ADD COMMENT • link 4.2 years ago by dumeir ▴ 20

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Have you tried using --allow-extra-chr without the 0?

Have you tried looking at line 938485, 938486, 938487 to see whether these lines are just broken somehow?

ADD REPLY • link 4.2 years ago by Philipp Bayer 8.3k

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Yes I've tried both of your suggestions. Those lines are in the exact same formatting, but just have IDs like "6_ssto_hap7". I tried changing one of those to just "6" and there was no error for that line.

ADD REPLY • link 4.2 years ago by dumeir ▴ 20

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Can you post the full .log file from your failed run? (Please make sure the version date/number is included.)

ADD REPLY • link 4.2 years ago by chrchang523 10k

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PLINK v1.90b6.14 64-bit (7 Jan 2020)

Options in effect:
  --allow-extra-chr 0
  --bfile <SNPfile>
  --extract <coordinates.txt>
  --make-bed
  --out <newfile>

Start time: Wed Jan 22 12:06:24 2020

Random number seed: 1579655184
8192 MB RAM detected; reserving 4096 MB for main workspace.
8146 variants loaded from .bim file.
571 people (0 males, 571 females) loaded from .fam.
571 phenotype values loaded from .fam.
Error: Invalid chromosome code on line 938486 of --extract range file.

End time: Wed Jan 22 12:06:24 2020

ADD REPLY • link updated 4.2 years ago by GenoMax 141k • written 4.2 years ago by dumeir ▴ 20

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Ok, it's erroring out because the chromosome code isn't in your dataset. This is a bug, "--extract range" should just ignore that line. I'll post a fix tonight.

ADD REPLY • link 4.2 years ago by chrchang523 10k

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Sorry, just realised I accidentally deleted "range" from --extract range in the log file when I was changing the txt file name

ADD REPLY • link 4.2 years ago by dumeir ▴ 20

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Bugfix is now posted.

ADD REPLY • link 4.2 years ago by chrchang523 10k

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Thanks for that. I no longer receive the error but I know there are SNPs within some of the bp ranges with unusual chromosome IDs and they're not being extracted, only chromosomes 1-23. I would still like to extract them.

I also manually manipulated the bp position files to increase the search window but now I'm getting this error:

Error: Invalid range start position on line 830868 of --extract range file.

Is there a way to ignore that these positions are invalid and continue searching anyway?

ADD REPLY • link 4.2 years ago by dumeir ▴ 20

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At this point, I’ll need you to send me a set of files to reproduce what you’re seeing.

ADD REPLY • link 4.2 years ago by chrchang523 10k

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For the record, the problem was a negative position value, resulting from subtracting 5000 from the original interval-start and adding 5000 to the original interval-end coordinates.

This will remain an error in plink 1.9 and 2.0. However, today's plink 2.0 build adds --bed-border-bp/--bed-border-kb flags which perform this interval-extension for you.