Entering edit mode
2.3 years ago
luckysardar171
▴
20
Hello folks,
I am trying see the allelic expression from RNA seq data for that I have used heterozygous SNPs from VCF file, using GATK asereadcounter got the SNPs count problem I am confused with a genes SNPs showing both biallelic count and monoallelic count any one suggest what will be the issue below giving some examples
ID Chromosome SNP Ref Alt gene_name
ENSMUSG00000033845 1 4774188 12 0 Mrpl15
ENSMUSG00000033845 1 4774538 10 0 Mrpl15
ENSMUSG00000033845 1 4775069 10 0 Mrpl15
ENSMUSG00000033845 1 4775803 10 0 Mrpl15
ENSMUSG00000033845 1 4776734 300 203 Mrpl15
ENSMUSG00000033845 1 4781549 2 8 Mrpl15
ENSMUSG00000033845 1 4782730 365 241 Mrpl15
ENSMUSG00000033845 1 4785703 122 136 Mrpl15
ENSMUSG00000033813 1 4857943 387 370 Tcea1
ENSMUSG00000033813 1 4896452 37 5 Tcea1
ENSMUSG00000033813 1 4896518 78 5 Tcea1
ENSMUSG00000033813 1 4897736 18 0 Tcea1
ENSMUSG00000033813 1 4897745 16 0 Tcea1
ENSMUSG00000033793 1 5095686 0 373 Atp6v1h
ENSMUSG00000033793 1 5124338 0 395 Atp6v1h
ENSMUSG00000033793 1 5162288 50 69 Atp6v1h
ENSMUSG00000033793 1 5162341 34 45 Atp6v1h
ENSMUSG00000033793 1 5162347 26 42 Atp6v1h
ENSMUSG00000046101 1 9941079 0 10 6030422M02Rik
ENSMUSG00000046101 1 9942048 9 13 6030422M02Rik
ENSMUSG00000036850 2 24974162 51 101 Mrpl41
ENSMUSG00000036850 2 24974614 0 482 Mrpl41
ENSMUSG00000036850 2 24974997 7 301 Mrpl41
ENSMUSG00000003131 9 45965680 0 88 Pafah1b2
ENSMUSG00000003131 9 45965880 0 163 Pafah1b2
ENSMUSG00000003131 9 45966221 93 48 Pafah1b2
ENSMUSG00000003131 9 45966516 108 106 Pafah1b2
ENSMUSG00000003131 9 45966539 139 101 Pafah1b2
ENSMUSG00000003131 9 45966968 0 332 Pafah1b2
ENSMUSG00000003131 9 45967403 0 240 Pafah1b2
ENSMUSG00000003131 9 45967446 0 296 Pafah1b2
ENSMUSG00000003131 9 45967547 3 207 Pafah1b2
ENSMUSG00000003131 9 45967758 0 36 Pafah1b2
Thank you
