Can some one give me a some heads up on how to approach this problem?
I read the vcf file and generated the following information (in text file). Now, I want to put back the phased information back to the vcf file.
contig pos ref haplotype_block hap_X hap_Y log_odds_ratio My_PG Sp_PG My_hap Sp_hap
2 2969 C 3706 T C -1.902 0 1 C T
2 3222 G 3706 G C - 1 0 C G
2 3416 G 3706 A G - 0 1 G A
2 5207 T 1856 T A 2.225 0 1 T A
2 5238 G 1856 C G - 1 0 C G
2 5398 A 1856 A G - 0 1 A G
2 5403 A 1856 A G - 0 1 A G
2 5426 C 1856 C A - 0 1 C A
2 5434 A 1856 A G - 0 1 A G
2 5467 C 1856 A C - 1 0 A C
2 5483 A 1856 A C - 0 1 A C
2 6636 C 892 T C 2.238 1 0 T C
2 6740 A 892 A G - 0 1 A G
2 12138 T 892 T A - 0 1 T A
2 12160 G 892 G A - 0 1 G A
2 12237 G 892 G C - 0 1 G C
2 12298 T 892 T G - 0 1 T G
2 12301 T 892 T A - 0 1 T A
I want to > read the same vcf file > match the contig and position > then write the new data into the FORMAT and SAMPLE fields.
I want to create new tag in FORMAT field and insert the corresponding value in SAMPLE field:
haplotype_block as HB
log_of_odds_ratio as LOD
phased_genotype as PG and insert the My_PG|Sp_PG
phased_allele as PA and insert My_hap|Sp_hap
I read through several examples and tried working this out, but I am not very clear on how to approach this problem. Any suggestions?
Can some one give me a some heads up on how to approach this problem?
I read the vcf file and generated the following information (in text file). Now, I want to put back the phased information back to the vcf file.
I want to > read the same vcf file > match the contig and position > then write the new data into the
FORMAT
andSAMPLE
fields.I want to create new tag in FORMAT field and insert the corresponding value in SAMPLE field:
I read through several examples and tried working this out, but I am not very clear on how to approach this problem. Any suggestions?
Thanks,