From: Heng Li Date: Mon, 13 Dec 2010 04:02:19 +0000 (+0000) Subject: * samtools-0.1.12-4 (r884) X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=7d93d105e56d3bcee4be728077716794dddf21e7;p=samtools.git * samtools-0.1.12-4 (r884) * fixed a long-existing flaw in the INDEL calling model --- diff --git a/bam2bcf_indel.c b/bam2bcf_indel.c index 239fb8d..3a8782b 100644 --- a/bam2bcf_indel.c +++ b/bam2bcf_indel.c @@ -113,7 +113,7 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla extern void ks_introsort_uint32_t(int, uint32_t*); int i, s, j, k, t, n_types, *types, max_rd_len, left, right, max_ins, *score1, *score2, max_ref2; int N, K, l_run, ref_type, n_alt; - char *inscns = 0, *ref2, *query; + char *inscns = 0, *ref2, *query, **ref_sample; khash_t(rg) *hash = (khash_t(rg)*)rghash; if (ref == 0 || bca == 0) return -1; // mark filtered reads @@ -188,6 +188,50 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla if (ref[i] == 0) break; right = i; } + /* The following block fixes a long-existing flaw in the INDEL + * calling model: the interference of nearby SNPs. However, it also + * reduces the power because sometimes, substitutions caused by + * indels are not distinguishable from true mutations. Multiple + * sequence realignment helps to increase the power. + */ + { // construct per-sample consensus + int L = right - left + 1; + uint32_t *cns; + char *ref0, *r; + ref_sample = calloc(n, sizeof(void*)); + cns = calloc(L, 4); + ref0 = calloc(L, 1); + for (i = 0; i < right - left; ++i) + ref0[i] = bam_nt16_table[(int)ref[i+left]]; + for (s = 0; s < n; ++s) { + r = ref_sample[s] = calloc(L, 1); + memset(cns, 0, sizeof(int) * L); + // collect ref and non-ref counts + for (i = 0; i < n_plp[s]; ++i) { + bam_pileup1_t *p = plp[s] + i; + bam1_t *b = p->b; + uint32_t *cigar = bam1_cigar(b); + uint8_t *seq = bam1_seq(b); + int x = b->core.pos, y = 0; + for (k = 0; k < b->core.n_cigar; ++k) { + int op = cigar[k]&0xf; + int j, l = cigar[k]>>4; + if (op == BAM_CMATCH) { + for (j = 0; j < l; ++j) + if (x + j >= left && x + j < right) + cns[x+j-left] += (bam1_seqi(seq, y+j) == ref0[x+j-left])? 1 : 0x10000; + x += l; y += l; + } else if (op == BAM_CDEL || op == BAM_CREF_SKIP) x += l; + else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) y += l; + } + } + // determine the consensus + for (i = 0; i < right - left; ++i) + r[i] = (cns[i] && (double)(cns[i]&0xffff) / ((cns[i]&0xffff)+(cns[i]>>16&0xffff)) < 0.7)? 15 : ref0[i]; +// for (i = 0; i < right - left; ++i) fputc("=ACMGRSVTWYHKDBN"[(int)r[i]], stderr); fputc('\n', stderr); + } + free(ref0); free(cns); + } { // the length of the homopolymer run around the current position int c = bam_nt16_table[(int)ref[pos + 1]]; if (c == 15) l_run = 1; @@ -251,23 +295,19 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla else ir = est_indelreg(pos, ref, -types[t], 0); if (ir > bca->indelreg) bca->indelreg = ir; // fprintf(stderr, "%d, %d, %d\n", pos, types[t], ir); - // write ref2 - for (k = 0, j = left; j <= pos; ++j) - ref2[k++] = bam_nt16_nt4_table[bam_nt16_table[(int)ref[j]]]; - if (types[t] <= 0) j += -types[t]; - else for (l = 0; l < types[t]; ++l) - ref2[k++] = inscns[t*max_ins + l]; - if (types[0] < 0) { // mask deleted sequences to avoid a particular error in the model. - int jj, tmp = types[t] >= 0? -types[0] : -types[0] + types[t]; - for (jj = 0; jj < tmp && j < right && ref[j]; ++jj, ++j) - ref2[k++] = 4; - } - for (; j < right && ref[j]; ++j) - ref2[k++] = bam_nt16_nt4_table[bam_nt16_table[(int)ref[j]]]; - for (; k < max_ref2; ++k) ref2[k] = 4; - if (j < right) right = j; - // align each read to ref2 + // realignment for (s = K = 0; s < n; ++s) { + // write ref2 + for (k = 0, j = left; j <= pos; ++j) + ref2[k++] = bam_nt16_nt4_table[(int)ref_sample[s][j-left]]; + if (types[t] <= 0) j += -types[t]; + else for (l = 0; l < types[t]; ++l) + ref2[k++] = inscns[t*max_ins + l]; + for (; j < right && ref[j]; ++j) + ref2[k++] = bam_nt16_nt4_table[(int)ref_sample[s][j-left]]; + for (; k < max_ref2; ++k) ref2[k] = 4; + if (j < right) right = j; + // align each read to ref2 for (i = 0; i < n_plp[s]; ++i, ++K) { bam_pileup1_t *p = plp[s] + i; int qbeg, qend, tbeg, tend, sc; @@ -406,6 +446,8 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla } free(score1); free(score2); // free + for (i = 0; i < n; ++i) free(ref_sample[i]); + free(ref_sample); free(types); free(inscns); return n_alt > 0? 0 : -1; } diff --git a/bamtk.c b/bamtk.c index da54ffd..613e76c 100644 --- a/bamtk.c +++ b/bamtk.c @@ -9,7 +9,7 @@ #endif #ifndef PACKAGE_VERSION -#define PACKAGE_VERSION "0.1.12-3 (r878)" +#define PACKAGE_VERSION "0.1.12-4 (r884)" #endif int bam_taf2baf(int argc, char *argv[]); diff --git a/bcftools/vcfutils.pl b/bcftools/vcfutils.pl index 5df8b0c..e38f1ca 100755 --- a/bcftools/vcfutils.pl +++ b/bcftools/vcfutils.pl @@ -215,7 +215,7 @@ Note: This command discards indels. Output: QUAL #non-indel #SNPs #transitions # } sub varFilter { - my %opts = (d=>2, D=>10000, a=>2, W=>10, Q=>10, w=>10, p=>undef, 1=>1e-4, 2=>1e-100, 3=>0, 4=>1e-4, G=>0, S=>1000); + my %opts = (d=>2, D=>10000000, a=>2, W=>10, Q=>10, w=>10, p=>undef, 1=>1e-4, 2=>1e-100, 3=>0, 4=>1e-4, G=>0, S=>1000); getopts('pd:D:W:Q:w:a:1:2:3:4:G:S:', \%opts); die(qq/ Usage: vcfutils.pl varFilter [options] @@ -289,7 +289,7 @@ Note: Some of the filters rely on annotations generated by SAMtools\/BCFtools. $flt = 1 if ($flt == 0 && $mq >= 0 && $mq < $opts{Q}); $flt = 7 if ($flt == 0 && /PV4=([^,]+),([^,]+),([^,]+),([^,;\t]+)/ && ($1<$opts{1} || $2<$opts{2} || $3<$opts{3} || $4<$opts{4})); - $flt = 8 if ($flt == 0 && ((/MXGQ=(\d+)/ && $1 >= $opts{G}) || (/MXSP=(\d+)/ && $1 < $opts{S}))); + $flt = 8 if ($flt == 0 && ((/MXGQ=(\d+)/ && $1 < $opts{G}) || (/MXSP=(\d+)/ && $1 >= $opts{S}))); my $score = $t[5] * 100 + $dp_alt; my $rlen = length($t[3]) - 1; # $indel_score<0 for SNPs @@ -312,7 +312,10 @@ Note: Some of the filters rely on annotations generated by SAMtools\/BCFtools. } else { # SNP or MNP for my $x (@staging) { next if (($x->[0]&3) != 3 || $x->[4] + $x->[2] + $ow < $t[1]); - $flt = 5; + if ($x->[4] + length($x->[7]) - 1 == $t[1] && substr($x->[7], -1, 1) eq substr($t[4], 0, 1) + && length($x->[7]) - length($x->[6]) == 1) { + $x->[1] = 5; + } else { $flt = 5; } last; } # check MNP