SNP plotting from VCF file in (non database) organism

Question

[justinfanyi]

Hello everyone,

I have called SNP and annotated;results in vcf format, I have been trying to work out visualization of this SNP using various tools like ggbio,circos,Gviz with no success since most pull their data from database like hg19,mm. I have the rice genome(fasta) and annotation file(gff3). Could anyone help me with displaying my variants in simple line graph(manhattan sort of) basing with chromosome1 to 12.Thanks.

VCF

#CHROM    POS    ID    REF    ALT    QUAL    FILTER    INFO    FORMAT    Co39.bam
Chr1    185892    .    A    G    61.0    .    DP=32;VDB=0.0057;AF1=1;AC1=2;DP4=0,0,23,0;MQ=50;FQ=-96;EFF=DOWNSTREAM(MODIFIER||1453||204|OS01G0103600|protein_coding|CODING|OS01T0103600-01||1),DOWNSTREAM(MODIFIER||3284|||NCRNA_17128|ncRNA|NON_CODING|NCRNA_17128||1),DOWNSTREAM(MODIFIER||3548|||NCRNA_795|ncRNA|NON_CODING|NCRNA_795||1),DOWNSTREAM(MODIFIER||3549|||NCRNA_46965|ncRNA|NON_CODING|NCRNA_46965||1),DOWNSTREAM(MODIFIER||358||219|OS01G0103600|protein_coding|CODING|OS01T0103600-02||1),DOWNSTREAM(MODIFIER||3738|||NCRNA_923|ncRNA|NON_CODING|NCRNA_923||1),INTERGENIC(MODIFIER||||||||||1),UPSTREAM(MODIFIER||1653||73|OS01G0103650|protein_coding|CODING|OS01T0103650-00||1|WARNING_TRANSCRIPT_NO_START_CODON),UPSTREAM(MODIFIER||64||130|OS01G0103400|protein_coding|CODING|OS01T0103400-01||1|WARNING_TRANSCRIPT_NO_START_CODON)    GT:PL:GQ    1/1:94,69,0:99
Chr1    228592    .    C    T    222.0    .    DP=82;VDB=0.0394;AF1=1;AC1=2;DP4=0,0,66,10;MQ=50;FQ=-256;EFF=DOWNSTREAM(MODIFIER||3049|||OS01G0104350|ncRNA|NON_CODING|OS01T0104350-00||1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T204M|267|OS01G0104400|protein_coding|CODING|OS01T0104400-01|3|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T204M|267|OS01G0104400|protein_coding|CODING|OS01T0104400-02|3|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T204M|267|OS01G0104400|protein_coding|CODING|OS01T0104400-03|3|1),UPSTREAM(MODIFIER||3736|||NCRNA_3527|ncRNA|NON_CODING|NCRNA_3527||1)    GT:PL:GQ    1/1:255,229,0:99
Chr1    13246715    rs351213482    G    A    222.0    .    DP=31;VDB=0.0447;AF1=1;AC1=2;DP4=0,0,12,19;MQ=50;FQ=-120;EFF=DOWNSTREAM(MODIFIER||1073|||NCRNA_13851|ncRNA|NON_CODING|NCRNA_13851||1),DOWNSTREAM(MODIFIER||2931|||NCRNA_12250|ncRNA|NON_CODING|NCRNA_12250||1),DOWNSTREAM(MODIFIER||4989|||NCRNA_46711|ncRNA|NON_CODING|NCRNA_46711||1),DOWNSTREAM(MODIFIER||657||772|OS01G0337500|protein_coding|CODING|OS01T0337500-00||1|WARNING_TRANSCRIPT_INCOMPLETE),UTR_3_PRIME(MODIFIER||267||906|OS01G0337600|protein_coding|CODING|OS01T0337600-02|26|1|WARNING_TRANSCRIPT_NO_START_CODON);RSPOS=13246715;SAO=0;VC=snp;VP=050000000000000000020100;dbSNPBuildID=138    GT:PL:GQ    1/1:255,93,0:99

Expected visual

(basically a wave graph) Y-axis(values {0.0-1.0} of FS-AFD4) X-axis{chr1 -chr12}

Or anything similar that can help display distribution of SNPs across the whole genome.

Thanks

[Pierre Lindenbaum]

"Expected visual" ?

[David W]

You image isn't displaying, as the url appears to be a path to the file on your own computer. You'll have to upload it somewhere else for others to see it @ biostars.

[justinfanyi]

Thanks for your replies,edited the question to show my intentions of the plotting!