Question: Trying to filter vcf file using SNPSIFT tool. It throws an error message
0
gravatar for bioinforesearchquestions
4.5 years ago by
United States
bioinforesearchquestions280 wrote:

Dear All,

I have been provided many vcf files generated using GATK. I am trying to filter the VCF file using filter option from SnpSift tools.

Before filtering the vcf file, I performed vcf validation using vcf_validator. I received following lines from it

INFO field at chr1:25639411 .. Could not validate the float [NaN]

INFO field at chr5:84948114 .. Could not validate the float [NaN]

.... INFO field at chrX:119015903 .. Could not validate the float [NaN]

I learnt from others that this is not a big issue for processing the vcf files for the downstream analysis. Do I need to perform any steps to rectify it?

I am filtering based on following conditions

  • Filter : PASS
  • Genotype: NonRef (0/1, 1/1, 1/2..so on)

command: cat inputvcffile.vcf.gz | java -jar SnpSift.jar filter "FILTER = 'PASS'" | java -jar SnpSift.jar filter "isVariant( GEN[0] ) | isHet( GEN[0] )" | bgzip -c > outputvcf.vcf.gz

Error:

VcfFileIterator.parseVcfLine(114): Fatal error reading file '-' (line: 1): ^_<8B>^H^D^@^@^@^@^@<ff>^F^@BC^B^@06<ed>}<eb>S#ɱ<ef>g<fc>W(<ec>^O<d7>ESCGh<ea><fd>И{C^C^LK<98>^A^F<d8><f1><f5>u8^T^Z^P<a0><b3>B<u+0092><d8><d9><f1>_^?2<eb>Ѫ<96><aa><d5> Exception in thread "main" java.lang.RuntimeException: java.lang.RuntimeException: Impropper VCF entry: Not enough fields (missing tab separators?). ^_<8B>^H^D^@^@^@^@^@<ff>^F^@BC^B^@06<ed>}<eb>S#ɱ<ef>g<fc>W(<ec>^O<d7>ESCGh<ea><fd>И{C^C^LK<98>^A^F<d8><f1><f5>u8^T^Z^P<a0><b3>B<u+0092><d8><d9><f1>_^?2<eb>Ѫ<96><aa><d5> at ca.mcgill.mcb.pcingola.fileIterator.VcfFileIterator.parseVcfLine(VcfFileIterator.java:115) at ca.mcgill.mcb.pcingola.fileIterator.VcfFileIterator.readNext(VcfFileIterator.java:166) at ca.mcgill.mcb.pcingola.fileIterator.VcfFileIterator.readNext(VcfFileIterator.java:56) at ca.mcgill.mcb.pcingola.fileIterator.FileIterator.hasNext(FileIterator.java:123) at ca.mcgill.mcb.pcingola.snpSift.SnpSiftCmdFilter.run(SnpSiftCmdFilter.java:295) at ca.mcgill.mcb.pcingola.snpSift.SnpSiftCmdFilter.run(SnpSiftCmdFilter.java:269) at ca.mcgill.mcb.pcingola.snpSift.SnpSift.run(SnpSift.java:372) at ca.mcgill.mcb.pcingola.snpSift.SnpSift.main(SnpSift.java:70) Caused by: java.lang.RuntimeException: Impropper VCF entry: Not enough fields (missing tab separators?). ^_<8B>^H^D^@^@^@^@^@<ff>^F^@BC^B^@06<ed>}<eb>S#ɱ<ef>g<fc>W(<ec>^O<d7>ESCGh<ea><fd>И{C^C^LK<98>^A^F<d8><f1><f5>u8^T^Z^P<a0><b3>B<u+0092><d8><d9><f1>_^?2<eb>Ѫ<96><aa><d5> at ca.mcgill.mcb.pcingola.vcf.VcfEntry.parse(VcfEntry.java:888) at ca.mcgill.mcb.pcingola.vcf.VcfEntry.<init>(VcfEntry.java:165) at ca.mcgill.mcb.pcingola.fileIterator.VcfFileIterator.parseVcfLine(VcfFileIterator.java:112) ... 7 more cat: write error: Broken pipe /var/spool/torque/mom_priv/jobs/5800932.SC: line 19: vcf: command not found

vcfs snp snpsift • 1.9k views
ADD COMMENTlink written 4.5 years ago by bioinforesearchquestions280
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1086 users visited in the last hour