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Agf:r:l:M:q:Q:uaRC:BDSd:L:b:P:o:e:h:Im:F:EG:6OsUsage: samtools mpileup [options] in1.bam [in2.bam [...]] -6 assume the quality is in the Illumina-1.3+ encoding -A count anomalous read pairs -B disable BAQ computation -b FILE list of input BAM files [null] -C INT parameter for adjusting mapQ; 0 to disable [0] -d INT max per-BAM depth to avoid excessive memory usage [%d] -E extended BAQ for higher sensitivity but lower specificity -f FILE faidx indexed reference sequence file [null] -G FILE exclude read groups listed in FILE [null] -l FILE list of positions (chr pos) or regions (BED) [null] -M INT cap mapping quality at INT [%d] -r STR region in which pileup is generated [null] -R ignore RG tags -q INT skip alignments with mapQ smaller than INT [%d] -Q INT skip bases with baseQ/BAQ smaller than INT [%d] -D output per-sample DP in BCF (require -g/-u) -g generate BCF output (genotype likelihoods) -O output base positions on reads (disabled by -g/-u) -s output mapping quality (disabled by -g/-u) -S output per-sample strand bias P-value in BCF (require -g/-u) -u generate uncompress BCF output SNP/INDEL genotype likelihoods options (effective with `-g' or `-u'): -e INT Phred-scaled gap extension seq error probability [%d] -F FLOAT minimum fraction of gapped reads for candidates [%g] -h INT coefficient for homopolymer errors [%d] -I do not perform indel calling -L INT max per-sample depth for INDEL calling [%d] -m INT minimum gapped reads for indel candidates [%d] -o INT Phred-scaled gap open sequencing error probability [%d] -P STR comma separated list of platforms for indels [all] Notes: Assuming diploid individuals. bam_mpileupmpileupgroup_smplwww w w(w0UVVTSS\\1PP,PPPPfsPswQP)U$UXUUw w  w  w w(w0w8wGUne \ \d\\\\>Z\h\\]\\\\&+\_b\w\PTd\&+\)Qv`_&__w_n\nT ^ ^^SQ_S_f^fV^^^]S]E^ESZ^h^^QV^^Q^^&\&+V_^{P##:P:dd{Q7 PPZP+_zAZ&+v_{T`N_NeQ _ _T _4___Z_oh__[____&+_D__w_tQ-8QmR38RzAZ&+4SSQSSq | ^K^z ] ]T ]4]]]R]A]]]&+]`\`XX] ] ]T ]4]]]R]]>Z]Y]]+]_w]]{+_{+_*ZQ P>UPPzQ VfVVVryVAVVVV&+Vze \ \d\\\Du\u~P\>A\\\&+\yVVVSPSPPPPzSSSe S P ^ P ^| ^ P S  PD S ^^4SP+S+4PQqSS_SSowS&+SGNUz _ q _q t S _T _ _PKS4___A_o___&+_ Q Uc g Ql q U @ X@ W PW d Xd g P XXPX " R- / Q|  R RR 5X58U8MPMSU "R-/QRZoRK Q Q UQUQQUQ&*Q/4UquQ[ b Rk R RRRU:<U Q: A Uwwww w(w0w8(w U!S&#y#S#$S((S;T;!VZ#z#V#'V((VS\P!!PZ#y#S#D$SD$K$P$$P((S#_#(_@""\""P"&#\Z#|#\#D$\'(\;"]&#~#]#(]I""]""Q""Q""]""R""]Z#~#]#D$]'(]"8"\8"E"U&#|#\((\!!P##V#D$V'(V* bam_mpileup,( 8bw&KPCO$bw&@"O$bw',AjrLe@rDh_ q Z QV(NQVGN<Dqz|_ h Zoq 4 _ h Zoq 4   | _ h Zo  _ h Zo  `x{ q4 q4q4Q P Yq D I A D I : A 4 7 ( - 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