varcode fails when it sees strange sequences in a vcf

[kippakers]

I've been working with 1000 genomes vcfs and they have the following unusual alternate alleles scattered throughout, which understandably anger varcode:

22 51179178 BI_GS_DEL1_B4_P2897_43 A 100 PASS
22 51068654 ALU_umary_ALU_12538 G INS:ME:ALU 100 PASS

gives:
AttributeError: '_SV' object has no attribute 'sequence'

I removed these lines to get it working (~1000 in chr22) but it would be nice if varcode just skipped these rather than dying.

[timodonnell]

Thanks, Kip. Do you have a link to the VCF?

On Fri, May 29, 2015 at 6:06 PM, kippakers [email protected] wrote:

I've been working with 1000 genomes vcfs and they have the following
unusual alternate alleles scattered throughout, which understandably anger
varcode:

22 51179178 BI_GS_DEL1_B4_P2897_43 A 100 PASS
22 51068654 ALU_umary_ALU_12538 G INS:ME:ALU 100 PASS

gives:
AttributeError: '_SV' object has no attribute 'sequence'

I removed these lines to get it working (~1000 in chr22) but it would be
nice if varcode just skipped these rather than dying.

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#88.

[kippakers]

Sure, ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20130502/supporting/functional_annotation/filtered/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5.20130502.sites.annotation.vcf.gz

[iskandr]

Related to #123 (we don't yet support structural variants)