User: a.james
a.james • 110
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- 3 years, 10 months ago
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Posts by a.james
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C: Error while parsing vcf file
... @Pierre Lindenbaum, apparently the issue is with vcf.reader parser doesn't suit for vcf 4.2 files. ...
written 12 months ago by
a.james • 110
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Comment:
C: Error while parsing vcf file
... No, I just highlighted it for bio-stars. There is no quote in real vcf file. ...
written 12 months ago by
a.james • 110
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Comment:
C: Error while parsing vcf file
... Here is the whole line which complaints,
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT TUMOR NORMAL
1 14748 . G C . alt_allele_in_normal;t_lod_fstar ECNT=1;HCNT=4;MAX_ED=.;MIN_ED=.;NLOD=29.34;TLOD=4.58;CSQ=C|non_coding_transcript_exon_variant|MODIFIER|WASH7P ...
written 12 months ago by
a.james • 110
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Comment:
C: Error while parsing vcf file
... Thats the first line of my vcf file I mean after header, and I am wondering 82, 2 is in int format isnt?
...
written 12 months ago by
a.james • 110
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... Hello,
I am trying to convert my multiple vcf file into a tabular format. And I am having error while parsing through each row of the file
here is part of the script,
for files in results:
Va_BM = vcf.Reader(filename=files, compressed=False)
for variant in Va_BM:
...
written 12 months ago by
a.james • 110
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... Dear All,
How would get a list with number exons for all non-coding genes?
Any suggestion would be really great
Thank you ...
written 13 months ago by
a.james • 110
• updated
13 months ago by
Pierre Lindenbaum ♦ 107k
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... The prefix for both the query bed file and genome file for chromosomes has no "chr". And so I don't think that the potential reason
...
written 15 months ago by
a.james • 110
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... I didn't get any error message. Whereas I got an empty vcf file (I mean there is header but no results). I am supposed to get a vcf file with read depth and all the information I asked in the parameter of command line. ...
written 15 months ago by
a.james • 110
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... Dear All,
I need to query a set of chromosomal positions towards a couple of BAM files, and I am using samtools mpileup for this.
Following is my command line,
samtools mpileup -L 1000000 -u -A -B -d 100000 -Q 0 -t DP -t AD -t ADF -t ADR -f GRCh37.fa --positions mybed.bed sample1.bam sample2 ...
written 15 months ago by
a.james • 110
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... 1. Thank you so much its very clear ..
2: Which version of GeneSCF are you using ? It looks like you are using V1.0 !!! , Yes you are right.
I have tried the both versions..And with the old version v1.0 has considerable overlap with pathways from other platform for comaprision study. This is the ...
written 22 months ago by
a.james • 110
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