I'm trying to use ssahaSNP for SNP/INDEL discovery. However, I only received homozygote cases. How do I find heterozygote via this program? Below are the 4 commands I used based the instruction from http://computing.bio.cam.ac.uk/local/doc/ssaha2.pdf
ssahaSNP allinput.fastq Sorbil.fasta -tags 1 > all_ssahaSNP.out
egrep ALIGN all_ssahaSNP.out | awk '{print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' > all_alignment.dat
egrep ssaha:SNP all_ssahaSNP.out > all_SNP.dat
parse_SNP all_SNP.dat all_alignment.dat > all_parseSNP.out
ssahaSNP allinput.fastq Sorbil.fasta -tags 1 > all_ssahaSNP.out
egrep ALIGN all_ssahaSNP.out | awk '{print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' > all_alignment.dat
egrep ssaha:SNP all_ssahaSNP.out > all_SNP.dat
parse_SNP all_SNP.dat all_alignment.dat > all_parseSNP.out
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