Comments (2)
ACEnglish
commented on July 24, 2024
1
The base SVs don't have an INFO/END defined.
For example, if I take the first entry from your base VCF:
##fileformat=VCFv4.0
##FILTER=<ID=PASS,Description="All filters passed">
##fileDate=99991122
##contig=<ID=2L,length=23513712>
##contig=<ID=2R,length=25286936>
##contig=<ID=3L,length=28110227>
##contig=<ID=3R,length=32079331>
##contig=<ID=4,length=1348131>
##contig=<ID=X,length=23542271>
##contig=<ID=Y,length=3667352>
##ALT=<ID=INS,Description=Insertion of novel sequence relative to the reference>
##ALT=<ID=DEL,Description=Deletion relative to the reference>
##ALT=<ID=DUP,Description=Region of elevated copy number relative to the reference>
##ALT=<ID=INV,Description=Inversion of reference sequence>
##ALT=<ID=BND,Description=Breakend of translocation>
##INFO=<ID=SVTYPE,Number=1,Type=String,Description=Type of structural variant>
##INFO=<ID=SVLEN,Number=1,Type=Integer,Description=Difference in length between REF and ALT alleles>
##FORMAT=<ID=GT,Number=1,Type=String,Description=Genotype>
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Hifi_60x_0.999_1_cute
2L 61980 idINS61980 a <INS> 30 PASS SVTYPE=INS;SVLEN=89 GT 1/1
And run it through htslib:
import pysam
import sys
v = pysam.VariantFile(sys.argv[1])
o = pysam.VariantFile("delme.vcf", 'w', header=v.header)
for e in v:
o.write(e)I get the error:
[E::vcf_format] Invalid BCF, the INFO tag id=4 is too large at 2L:61980
Traceback (most recent call last):
File "/Users/english/code/truvari/tickets/long/tmp.py", line 8, in <module>
o.write(e)
File "pysam/libcbcf.pyx", line 4482, in pysam.libcbcf.VariantFile.write
File "pysam/libcbcf.pyx", line 4519, in pysam.libcbcf.VariantFile.write
OSError: [Errno 22] b'Invalid argument'
But when I add INFO/END:
##fileformat=VCFv4.0
##FILTER=<ID=PASS,Description="All filters passed">
##fileDate=99991122
##contig=<ID=2L,length=23513712>
##contig=<ID=2R,length=25286936>
##contig=<ID=3L,length=28110227>
##contig=<ID=3R,length=32079331>
##contig=<ID=4,length=1348131>
##contig=<ID=X,length=23542271>
##contig=<ID=Y,length=3667352>
##ALT=<ID=INS,Description=Insertion of novel sequence relative to the reference>
##ALT=<ID=DEL,Description=Deletion relative to the reference>
##ALT=<ID=DUP,Description=Region of elevated copy number relative to the reference>
##ALT=<ID=INV,Description=Inversion of reference sequence>
##ALT=<ID=BND,Description=Breakend of translocation>
##INFO=<ID=SVTYPE,Number=1,Type=String,Description=Type of structural variant>
##INFO=<ID=SVLEN,Number=1,Type=Integer,Description=Difference in length between REF and ALT alleles>
##INFO=<ID=END,Number=1,Type=Integer,Description=End position>
##FORMAT=<ID=GT,Number=1,Type=String,Description=Genotype>
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Hifi_60x_0.999_1_cute
2L 61980 idINS61980 a <INS> 30 PASS SVTYPE=INS;SVLEN=89;END=61981 GT 1/1
I do not get the error.
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jyw-atgithub
commented on July 24, 2024
Thank you!!
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