Measure cytosine retention and SNP test

pileup human TCGA WGBS NIC1254A46 focal

$ biscuit pileup -i NIC1254A46.bam -r hg19.fa -g chr20:29570686-29570686

returns

chr20  29570686  .  G  Y  46  PASS  NS=1;CX=CG;N5=ATCGG  DP:GT:GP:GQ:SP:CV:BT  15:0/1:14,4,37:46:G9,Y4:4:1.00

$ biscuit pileup -i NIC1254A46.bam -r hg19.fa -g chr20:26138808-26138808 -v 1 -n 999

returns

chr20  26138808  .  G  Y  5  PASS  NS=1;CX=CG;N5=TTCGA  DP:GT:GP:GQ:SP:CV:BT  45:0/1:15,14,147:5:G35,Y6:18:0.72
    DIAGNOSE;RN=13;CN=5;Bs0=GGGGGGGGGGGTTGGGGTTTTGGGTG;Sta0=88888888888448888444488848;Bq0=:<8<<8<<<<<<:889:9<9988888;Str0=--+++++--++----++--+++-+++;Pos0=61,56,53,51,40,38,37,37,27,20,20,20,19,18,14,11,10,10,10,6,6,3,3,2,1,1;Rret0=4,6,6,6,8,8,8,8,8,10,10,9,9,10,10,11,11,10,10,10,10,12,12,12,11,20;Bs1=AAAGGGGGGGGGGAGGAAG;Sta1=7776666666666766776;Bq1=;;;:;;;;<<<<<<78;99;Str1=+++--+---++---++---;Pos1=75,70,69,67,64,63,62,61,48,45,39,27,19,13,12,6,5,4,3;Rret1=9,10,10,11,12,12,13,13,13,13,13,17,15,11,16,17,15,15,18

$ biscuit pileup -i NIC1254A46.bam -r hg19.fa -g chr20:25847708-25847708 -v 1

returns

chr20  25847708  .  G  Y  20  PASS  NS=1;CX=CG;N5=TCCGT  DP:GT:GP:GQ:SP:CV:BT  16:0/0:4,8,60:20:G13,Y1:5:1.00
    DIAGNOSE;RN=5;CN=0;Bs0=GGGGGGGGGGT;Sta0=88888888884;Bq0=79;;:.<9<8<;Str0=+++-+---+-+;Pos0=74,70,65,59,55,50,40,40,36,25,14;Rret0=20,20,23,19,22,13,21,18,22,22,12;Bs1=GGGGG;Sta1=66666;Bq1=9:<<:;Str1=--+-+;Pos1=69,49,46,37,13;Rret1=18,16,17,17,19

$ biscuit pileup -i NIC1254A46.bam -r hg19.fa -g chr20:29425717-29425717 -v 1

returns

chr20  29425717  .  G  A  37  PASS  NS=1  DP:GT:GP:GQ:SP  30:0/0:5,14,111:37:G25,A2
    DIAGNOSE;RN=5;CN=3;Bs0=GGTGGGGGGGGGGGGGGAAGGG;Sta0=8848888888888888800888;Bq0=8<8;::=;8<<<<<<8*;;:;/;Str0=-+-+-+--+-----+--+++--;Pos0=97,76,73,66,65,62,60,59,58,50,47,44,39,37,24,22,17,15,14,8,4,4;Rret0=16,17,13,15,15,16,22,17,17,16,15,16,17,17,20,19,19,17,18,19,18,14;Bs1=GAGGAAGG;Sta1=67667766;Bq1=998;<;9;;Str1=--++-++-;Pos1=95,72,61,56,31,27,9,9;Rret1=13,12,11,8,9,10,9,9

somatic pileup

$$ biscuit pileup -i tumor.bam normal.bam -r mm10.fa -g chr19:1-3100000 -o mouseAPC.vcf -T
$$ bgzip -f mouseAPC.vcf
$$ tabix -p vcf mouseAPC.vcf.gz

single pileup

pileup mouse WGBS Smadh3 chromosome 19 and chromosome M

$$ biscuit pileup -i mouseSmadh3.bam -r mm10.fa -g chr19:1-3100000 -o mouseSmadh3.vcf -q 3

pileup human TCGA WGBS NIC1254A46 chromosome 19 and chromosome M

$$ biscuit pileup -i NIC1254A46.bam -r hg19.fa -o NIC1254A46.vcf -q 10